I have modded many seat brackets, built custom ones, etc and never once was asked about the mods, missing caps, etc...I would not worry about it, just make it fit you better
Lucky I am only 5'8' so on the lowest setting I am OK but if needed I would lower them in a heartbeat.
Take a good look under the seats lowered all the way, see how much lower you can go, might be able to cut them off and both together at the right height. I have done so and used steel plates on both sides, grade 8 bolts, etc with no worries. I have also welded some up when needed. I do not trust shops so DIY always but if trust them and the price is not crazy then go for it.
Rick
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2003 4runner LTD, V8, AWD, mild mods planned
2007 4runner LTD, V8, AWD, nicely modded, went to daughter when we went full time RV, had to have another one