The problem largely comes from when people are buying a new axe and condemning it based on the handle not being absolutely perfect, or buying a replacement handle online and then being similarly indignant. If you're at a brick and mortar shop and have the opportunity to rifle through several examples yourself, by all means go for the best you can. It's just that when things are left to chance to a certain degree, then being all fussy about minor flaws in a perfectly serviceable handle is silly. Use it 'til it breaks, then put a better handle on it. You may find that you go your whole life without ever needing to change out the original "flawed" handle, and there are tons of examples of well used vintage axes that attest to it.
Striving for perfection is a worthy goal, but perfection can be hard to find in a mass-manufactured natural product, and just because a handle isn't perfect doesn't necessarily mean that it's not good enough. There's been a large upswing in the number of mostly inexperienced folk (so they don't have the experience in using less-than-perfect axes to realize better) that rigidly demand perfection when they're just going to be using the axe recreationally for camping and other light duties. If using it as a shared professional trail worker's tool then the demands put on it are certainly going to be much higher and therefore higher quality becomes a prerequisite. If you have a handle that's on the lower side of quality without being a truly defective one then I just wouldn't spend much time lavishing it with detail work and use it with the expectation that it might fail at some point. Get a replacement handle ready to go for it so you aren't put out if the thing busts on you while working, and just use the one that's on it until it goes. I have a little 350g Calabria axe with a long skinny (less than 20mm thick at its thickest point) beech handle that has some small knots in it, and yet I've been using it for months without fear of failure because the handle is replaceable. If it breaks, I'll just pop another handle on it.
The way I see it, there's the ideal you strive for and then the actual requirements of the tool. Shoot for the best, but if you fall short of that mark then if it's within the real needs for the tool, then there's not much reason not to live with it. It's the latter part that many seem to struggle with these days and tends to irk me. Everyone likes perfection, but few actually require perfection even though they demand it.