It is possible to weld the joints so they are utterly smooth, but it is unlikely you have run across that kind of skill often. Some smooth joints you see may be fillet brazed. Another approved technique in fabrication, is to tig weld the joint, then "bondo" it with brass. This is common in general, but since at the loads we are talking about one can use brass to braze the joint in the first place, it would not be useful on bikes. In a situation where you need full penetration weld on 1/8" material and a smooth look, it's the done thing.

Bondoing a tig joint, is totally OK, but we don't tend to see it with bikes, because: a) There is a prejudice against non-metal finish on joints; b) On quality TIG, particularly custom, guys like to flaunt the quality of their work; c) On cheap stuff they don't care. I have used 5 minute epoxy and micro balloons with success on non-bikes, I like the adhesion epoxy gives, needs to be the good epoxy though, like WEST, DEVCON, etc... The epoxy approach is ok for joints, for larger areas you need a specialty product that allows blocking out the finish. Also, with any of these products the coat needs to be thin, so the underlying welds need to be clean. too lumpy and the coat required to hide the mess will probably pop off. Powder coat won't stick to bondo and may melt it, though there are special fillers for that. On a one off it would be cheaper to brass it.

Filing is bad for 2 reasons, one, cuts through the grain structure are bad for the weld. These are essentially porous free form castings, and interrupting the grain structure is to weaken it. Or something. The welds might still be strong enough, but you are undermining them, and since additive processes are cheaper, why do it. Second reason is you may end up cutting into the adjacent tube.

Other part of your post might get more attention on the vintage forum.