Since OE rubber bump stops compress a bit but don't move or have "travel," I'm assuming that when you say "factory bump stop travel" you mean "bump stops compressed onto the axle housing strike plates" or "preserving the OE bump stop location" (not relocating the contact point with a bracket or longer custom bump stop).
If so, you are 100%, spot on correct.
If you use a stock wheel you probably won't have a problem with a 12.5" wide 35. If you use wide wheels and/or wide 35's like a 13.50, you may run into clearance issues - especially on the back corner of the fender well, right behind the front tire, when turning. The idea behind wheels that stick wide aftermarket tires further out is to keep them from rubbing the radius arm/control arms at full-lock steering. The diameter might be fine at "full bump" meaning the top of the tire may not hit the plastic fender liner with the tires pointed straight ahead. But when you turn the truck, there may be interference. There are so many variations of tires and wheels out there (and many combinations of the two) that it's hard to say what will work or won't without a lot of research.
Exactly as you state, with a leveling kit, absolute tire clearance is still determined by the bump stop, but by effectively moving the axle down, you will have more tire clearance initially - before the wheel starts moving up into the wheel well. We call this "dynamic tire clearance."
With enough dynamic tire clearance, you can confidently run bigger rubber even though your absolute tire clearance hasn't changed - which is always determined by bump stop location - kind of like absolute ground clearance is determined by tire diameter.
I learned about this in a funny way. I was prepping the KORE race truck before the Baja 1000, we were moving up from 37x12.50 General tires to 39x13.50 BFG tires, so i was told to test for interference. I had the springs off the shocks and with the suspension fully-compressed and the steering at full-lock the tires would smash right into the stainless exhaust headers. I told Kent (the owner) about this and he just laughed at me and asked, "think of the speed and force required to bottom the truck, then imagine that speed and force equation happening instantly with the steering at full lock."
I was like, "yeah - we would have bigger problems than smashed headers - like a corner ripped off or an end over end rollover!" hahahah!
Anyway, it's the same with a stock truck. That's the best I can explain dynamic tire clearance.
You can see where the headers are relative to the tire. The tires never hit them.