I'm thinking of getting a guitar with a bolt-on neck, so that I can later get a second neck with a fretless fingerboard, and switch out those necks as needed. Would this potentially cause some kind of issue with the neck not being aligned right to the body or something after changing it out so many times?
I'd give up on the idea before you even start.
Sure, you can change necks, assuming both are compatible, but unless both fit perfectly, with almost zero movement tolerance, you'd have to line the whole thing up again. They'd each need a different action & each would have been resting without tension while the other neck was on, meaning you'd need to reset the neck relief each time.
You're also likely to mess up the threads eventually - screws into wood are really not designed to be removed & re-inserted multiple times. Something will eventually give.
If you were measuring that task as a paid job, you'd see it would quickly add up to the price of a whole new guitar. Consider it a day's job every time.
First you need to find two necks which both are a snug fit to that body. And also both have approximately the same angle into/onto that body. After swapping necks, a set-up would be needed, which may well entail trussrod adjustment and fettling at the bridge.
Obviously strings would need to be changed each time, and the holes which the screws that hold the neck on would suffer wear - and of course they would need to be exactly the same centres of each neck.
Time taken changing all that? A waste in my opinion. Another guitar would seem to be a more sensible solution - and then, you could have appropriate strings on each, and not wait the day or o whilee the neck hange settled in, let alone the wasted time doing the change.
Sorry, but a great theory (like so many), but impractical. Better to look for a pre-loved guitar, and maybe extract the frets from that.
I'm strongly in the "get a specific guitar for that" camp, too.
A thing with with fretless guitar is that you don't need to get over the frets, so you go with a very low action; lower than you could ever expect with frets. And because you don't need to bend — you can just slide as high as you want — you can play heavy strings without "working so hard", like BB King told Billy Gibbons.
This means that switching back and forth involves changing intonation, bridge height, string gauge and likely winding type, pickup height; basically, everything that can be adjusted on a guitar. Get a guitar, decide "This will be my fretless guitar", set it up knowing it's will get your fretless guitar, and use another one when you need to fret.