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Sorry if this is unorthodox and weird...

I assume you're having a lined fretless? If so, buye small white circular price stickers from an office supply store and put them in the center of the board from side to side and midway between the fret lines. On a four string, the dots should fall between the D and A strings (except for fret 12), so the strings shouldn't touch them to wear them off. You're going to have to get used to putting your finger on the fretline rather than in the middle, though, if you want to play in tune.
 
Use stickers if you must. Please don't go attempting surgery on the fretboard unless you're a serious craftsman, and even then best not to: the fretboard on a fretless bass is where it all happens, and you need a strong, even, consistent surface.
 
If the bass has white lines on the top of the neck that you can see, that would be the idea thing to go by. I find myself too often actually tilting the bass back at an angle to see those dots, then remind myself that I need to look at the lines instead so I won't tilt it back, which could effect my playing.
 
Seriously, man. Lay on some stickers. If they get bunged up by the strings clean them off and stick some new ones on. Change them weekly for that matter. Craft stores are full of that crap. I vote for gold stars like the ones my elementary school teacher used to stick on the smart kids papers.

If I understand correctly the VM has a plastic fingerboard (and I mean that in a good way, it's a cool idea) so you'd have to work hard to screw that up with stickers.
 
But I think I want a fretless, so I was looking at the Squier VM, and the one thing that keeps me from buying it is that I would like to have inlays on the fretboard. Now, I'm not going to spend that much money to put inlays in, so if I bought it, is there a cheaper way to put dots on the fretboard?

I feel exactly the same way.
I bought one anyways a while back, but the lack of inlays always bugged the crap out of me.

Having no inlays on a fingerboard has got to be the cheapest/dumbest look ever unless it's an unlined board or a classical guitar with no side dots.

I would try to paint some inlays on there rather than using stickers. Stickers can peel off and leave sticky residue, but paint should work pretty well as the strings shouldn't be contacting the paint layer unless you are using improper bending techniques.