It's all context when it comes to insurance companies and aftermarket mods.
Example, I work in a collision shop. If a Jeep comes in to us, 3 inch lift, 35' mud tires. Got T-boned at a light. The adjuster, if one even comes to look at it won't care. The mods did nothing. He won't replace any broken aftermarket stuff. But I can also count on 1 hand the amount of times things like that have come up in 5 years in the shop. (edit) Things like that being aftermarket stuff needing replacement. Suspension damage is usually light in collisions, especially with Jeeps.
Conversely, if someone was say...Touring back the Myra Rd, 3 inch lift, 35'' mud tires, broke through a bridge, had their shit hauled halfway out of the river on it's side and dragged back to civilization...well then an adjuster may have some more interesting things to say about it. Nothing is for sure of course, it all depends on the adjuster himself.
He may all out deny coverage. It may be raining that day, no one at the shop it was brought to is available to do a tear down. Means he'd have to rip it down in the lot, in the rain to do a proper estimate. In that case he's gonna give it a 'drive by estimation'. Which means he's gonna rubber stamp whatever the hell the shop wants to do to fix it.
Hell, 75% of things we get in at the shop at processed through our in house estimators. Their whole job is to make sure that it gets fixed, and insurance pays for it. not a chance in hell one of them mention after market parts unless they need to replace them.
So really, you're pretty damn safe when it comes to modding things and insurance companies. There exists a chance for you to get royally ed, but it's very small.
With the caveat that this all assumes your mods aren't over the top. If you're rolling 44 inch boggers on a 7.5 longarm lift and your shit looks more like a buggy then a Jeep you're going to get shit on. Hard.
Edit #2-- Did I once haul a blue XJ belonging to a guy named Jamie out of the woods in Waverly with you? Round midnight, blinding snowstorm.
Edit #3-- Asked the guy with the XJ. Yeah that was you. Nice to see you still wheeling it.