Do you still have your factory rails? I'd put them back on and make it look as original as possible and take it to toyota like "wtf"
Specialty glazier here, 15+ years of working with every type of sealant in the book. Good neutral cure silicones are better than any butyl for most purposes. You can get skinning or non-skinning butyl sealants and they do have their place, esp when it comes to bonding to rubbers. I'd pick them over a polyurethane and maybe even some hybrids for weatherproofing a truck. But for painted or non-ferrous metals you won't do any better than a neutral cure silicone like Dowsil 795 (1st choice) or 995, GE Silglaze or SCS, Durasil, etc.
I've peeled neutral cure silicone out of joints 30+ years old in full southern sun exposure that was still fully adhered, and installed hundreds of systems up to 30k sq ft of full exterior exposure sealed only with NCS. I've also seen it fail almost immediately if not properly installed, like any sealant, mostly related to issues that wouldn't arise in automotive/homeowner situations - too thin over a wide joint, not bonded to edges of joints, not accounting for metal expansion over a long run of flashing, and so on. Prep is important, clean with alcohol, naptha, or other residue-free solvent if not dealing with fresh surfaces.
Even most of the acetoxy silicones around today are pretty durable, and very UV resistant. Years ago that wasn't always the case. Never used Permatex for anything other than gaskets though.
On the main topic, years ago I built a custom roof rack, sealed the 4 holes in the roof with 795 and never had a leak, owned for years. I've also used it around several windshields in place of weatherstripping. But that's just a footnote compared to the thousands of gallons of the stuff I've used in some of the most extreme conditions you could imagine.
Windshields are installed with urethane, not butyl.
Just want to join in and say that I think the majority of this issue is dissimilar metal (galvanic) corrosion. The poor sealant probably didn't help, but that corrosion is incredibly aggressive.
Show your work.
Galvanic corrosion concentrates and can even accelerate corrosion. Notice how the corrosion is focused on the mounts on the underside of the roof? Nothing else shows corrosion, including the coated bracket. Any small amount of water that leaked inside exacerbated the issue as they likely carried electrolytes with them.
Source: background in corrosion/coatings.
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Yes, galvanic corrosion is on display here. But it's not the root cause of the issue. If it were, everyone with factory hardware and factory racks would have their roofs rusting to pieces (steel hardware has higher galvanic potential than sheet steel). But they're not.
I'm a new owner so I haven't pulled my headliner down yet, but is the stock hardware bare metal on a coated metal?
Update and supplier info since thought I got a couple PMs (and thought I responded at some point but they seem to have disappeared from my inbox and nothing ever shows up in sent folder, so apologies if not, been super busy this year).
I installed a Sherpa rack a few months ago and did end up using skinning butyl (PTI 757). The Sherpa racks, or at least the Quandary for GX470 uses a very hard rubber/EPDM block as a spacer/sealer in channel, below mounting bracket. I'm not confident that this block is able to compress enough to seal out all water, although would probably stop most of it. My paint was dinged up from factory rack bolts which would provide several possible channels for water too seep in, and of course the roof itself is a light radius whereas the blocks were square. IMO for weatherproofing these should've been silicone blocks, more pliable. That might've come at the expense of load capacity although there are metal sleeves through it, around the bolt, so probably wouldn't matter too much. Anyway, silicone won't bond well to EPDM so I used butyl after scrubbing the scum out of channels. If the blocks were silicone I could've used silicone sealant.
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Here's a pic of one corner of the custom roof rack setup I installed using Dowsil (then Dow Corning) 795 10ish years ago, it never leaked.
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Non-skinning butyl is available without a commercial account through DK Hardware (a CR Laurence reseller). PTI brand is hit or miss there but CRL 777 is comparable to 757 and skinning, 707 is non-skinning (don't let them tell you 757 and 707 are the same, their computer is wrong). Elastiseal B100 is another decent skinning butyl, bp300 is non-skinning.
Neutral cure silicones and many other specialty sealants are available without an account through White Cap/Kenseal or, I believe, through Garvin Construction Products. All of the above will ship. Tremco Spectrem 2 is comparable to Dowsil 795 and a few bucks cheaper, other options in previous post.
[MENTION=58630]jbtvt[/MENTION] I think I understand the difference between skinning and non-skinning, but I'm struggling to understand what you are recommending. It looks like you used skinning for the Sherpa block, but I thought non-skinning would stay soft and flexible and be a better seal. Do I have that backwards?
For a joint under compression like this you're right that non-skinning would be a better choice from a strictly waterproofing perspective. In practice I don't think it'll make a difference over the lifespan of the truck. IME butyl fails at a higher rate than silicones but usually (or always from what I can remember now top of head) due to the tendency to sag which isn't an issue here since it's basically FIPG. Never seen adhesive failure with it. So as long as the rubber spacer is set before butyl skins over I don't think it will matter, but time will tell.
My main reason for using skinning was that non-skinning always makes such a mess, so when I pull the weatherstripping out in a few years to check on things or clean the channels my roof and hands and every other thing within 300' won't be covered in butyl strings. Years of demolishing old systems with that stuff has given me PTSD. Skinning also remains pretty flexible, although not nearly as much joint movement capability as a quality silicone, it just doesn't stay as runny as the moment it came out of the tube like the non.
Unless you need to bond to rubber I would 100% recommend a neutral cure silicone either way. In old rack pic above I had 5 metal-to-metal joints at each corner of the rack - washer to washer/bolt/roof, and no leaks. And less mess than even skinning butyl, and you can reuse the extra around your windshield, or shower corners, or chimney flashing, etc