Fret problem with my Warmoth G-5 Bass

Look closely at the end of the fret with magnification and bright light. Is there a gap under the fret in either side of the tang? If so, you could give it a light rap with a hard plastic mallet; don't use brass or steel.

One thing that might work for a long fret rocker is a stamped steel rectangular blade of a pancake flipper.

If you use something like a nut file, machinist's ruler, or other tool that is going to be darn close to straight but not dead on precise, a good trick is to try both sides. Usually if one side is a bit concave then the other side will be a bit convex, so if you get the same result with both sides... well, it won't guarantee anything, but it increases the probability of your deduction. I don't doubt your diagnosis, but if you get snagged and want to double check it, that can help.

Warmoth fingerboards are more prone to being kinda wavy and dippy at times because they really like having that super polished look, and can get carried away. If that was the cause on this, you'd have more faint buzzes and they'd occur in a few places. Having just one big culprit does point towards a fret. As Peegoo says, you should see a clear gap if that is the case. They use a fret arbor, and they can often get hung up on junk in the slot without telegraphing through the handle, and can be easy to miss.

If you decide to hammer it, use a soft faced hammer. I like to hit closer to the center, and sort of drag the hammer out towards the edge through the stroke. It is easier to do than to describe, but you'll figure it out. If you hit direct on the corner, you can mush it. You're extra likely to do that because they glue the frets, both in the slot and under the tang, so you'll have to fight that a bit. You'll know you dropped the fret when that bit of glue pudges out a bit. You can just knock it down with a file or sanding sponge.

If you still don't have any luck, look at the first fret and see if it looks crunched into the wood. It might be hard to see, because if they did this, it can be easy enough to cover up their tracks in the fret end dressing process. Hitting the arbor too close to the edge of the fingerboard can do this to a neck, as would using the incorrect radius caul. It isn't likely given the width of the neck (they tend to just slide out of the cradle) and hardness of the fingerboard, but hey, worth checking if you get stumped.

They do smooth out the fingerboards with a medium grit free-cut on an orbital sander. It doesn't result in a gloss, so much as smooth, bare wood, removing any signs of sandpaper marks, except maybe the rogue orbital tail. It isn't that dramatic, and IMO not worth the effort. When I do a refret, I sand with the gain up to either 220, 320 or 400 depending on the density of the fingerboard material, and I get a great looking fingerboard without the orbital issues. But, that's a tangent waiting to happen.

The glue does harden, but they use a gel type and it remains a bit plastic-like when it dries. You won't make the fret "bounce"... that can happen with some guitars, usually ones with oversized slots or frets that are bent out of whack before you even get to them. Sometimes that happens with Epiphones and similar instruments, and they have to be clamped and glued to stay put. That won't be the case for you... if anything, the slots are too tight, and since it was done on an arbor, they won't be bent strangely. You likely won't bend it out of whack if you stay away from the hard faced hammers. Even with the thin type super glue which hardens to approximately what you get with a hard poly finish (not identical, but that's yet another tangent) you can still mush it with some hammer hits.

Stainless is less likely to conform to radius irregularities or be generally forgiving, so it makes sense it would be a bit high. If someone is incredibly thorough with their fretting it will make little difference which material they use, but the bottom line is that you HAVE to be thorough on that stuff with stainless... so, if you're hearing mixed reports about how easy or difficult stainless is, that's why. For your hammering, it won't change stuff too much. If you were to mangle the fret, it becomes harder to go back and fix what you did, but I don't think you're more likely to mangle it. Honestly, the fret is down enough that it won't have enough travel to be a problem. If you were putting the whole fret in, it would be a different matter, but you're just love-tapping. In fact, you could get away with a hard faced hammer with this, but if it makes you nervous it is best to stick to a soft faced one.

a .046" will be fine. The only time a nut will be finicky about very small amounts of being over sized is when the break angle is horrible. On a bass, that's the classic A string on a J or P bass that doesn't go down far enough. Your angled peghead will be just fine.

I'd put something between the neck and the block... you PROBABLY won't leave a mark since you're hitting lightly and wenge is harder than that block, but some thin leather or cork or something would give you the peace of mind. Lacking those things, a very soft wood like balsa or basswood can be good, too.

Leaning on the neck a bit to keep it from recoiling might help, too.

You can go pretty oversized with the file and achieve good results if you have to; you're making a round-bottomed slot after all. I usually try to use one that's around .005 over but you can use your .046, just angle it back and forth a bit to give it a little more width if need be. You can mark the slot with pencil to see what you're doing if ya want.
FWIW the few times I've had a popped fret at the edge like that tapping 'em in never worked, I ended up gluing and clamping. Hopefully it works for your situation.