I hear you, and I considered a number of locations for the Blue Sea box. Everything from right above the existing fuse box in the engine bay (like your build), to right next to the driver side fender hinge (sleepydad), to under the rear seat (kolelt), to all the way back to the rear cargo panel (violation).
I'm leaning towards the under dash location because in my case, that's where most of the loads will tie in - seat heaters, mirror heaters, power outlet circuit, etc. So I'll have one big 8 ga wire come through the grommet to the fuse box, but then the individual load circuits will tie right into the box without having to go through the grommet and into the engine bay.
I've always read that you want the fuse box to be closer to your loads, not to your supply. Sort of like why you put a subpanel in a home if you want to have a bunch of breakers in a distant location, and run a big cable from the main panel to the subpanel. So if most of my loads were under the hood, I'd probably mount the fuse box there, but I think mine will mostly be in the passenger compartment.
In the end I think it's a toss up (it's only about a three foot difference in cable length), so provided the cable is sized adequately, it doesn't make a difference. I did think that it'd be nicer to have the fuse box away from heat and moisture, so that's why I'm leaning towards the under dash area.
I do think that I may move the 100A relay into the engine bay, near the circuit breaker. First, I bet that sucker is loud when it clicks (I'll test it tonight), so I don't know if I want that clicking under my feet every time I start the truck. And second, it would mean that the portion of cable in the engine bay from the relay to the fuse box under the dash will not be "live" when the key is off. I don't really see an issue with having a "live" cable (the starter cable is "live" too if you decide to cut through it

), but it does seem like a small benefit, so why not.
What do you think?
That's quite the spaghetti of wires! I actually did consider pilfering a newer (99+) harness and fuse box for my '97, thus getting the OEM fog light, heated mirror, and power outlet relays and fuses that mine doesn't have - but in the end decided it's too much of a project. You're obviously braver than me!
I do plan to snag a long section of an OEM harness at the junkyard to have some OEM wires on hand. Just makes the job look cleaner IMO.