FWIW, I view the screen covering the taskbar as a bug in JWM. Very annoying to constantly be moving windows to get to the taskbar and/or access to the menu. IMO JWM is best run with taskbar at the bottom (emulates Windows 9x) as not everything works very well when at the top.
But size alone is reason enough. I hope you read the message link above. And by looking at the requirements of jwm-snapshot even more so.
It's not a "bug" but is related to a setting in .jwmrc-tray. The default for the tray in jwmrc is 8 but TC has the tray factored out and layer set at 3, which means anything with a layer set >3 will go above the tray. I was tired of stuff covering up my tray so I reset it to a higher number -- 12 is absolute but even 8 should suffice unless you set specific apps to a higher number. I didn't know who set that up but figured it was so someone could get more space on a screen. I don't use title bars for most apps so I don't need anything greater than the layer for the tray.
Once that setting is appropriately set to a higher number, it doesn't matter if you set the tray on top, bottom, or either side. It should work quite well under any circumstance.
As far as jwm goes, we don't have to use the snapshot or even use jwm configured for all options whether it's in the base or not; I'll most likely use my own (older) version of jwm without any of the image libs or stick with ratpoison or ion. No matter how it's configured and compiled, jwm is still bigger than is needed for TC's base. I also don't care for the direction it's going, but such is life in open source: add new system requirements and call them "features." What's it doing now that it didn't do before? Any way to change the menu without restarting it? Or does it have a feature beyond the tray list of open windows? Or is it all a bunch of window dressing that's only aesthetic and not functional?
The base of TC should only be what's essential to get a bare minimal desktop, and for that flwm is more than adequate -- it has a menu, it provides window decorations to make managing things simple, and so on.
Not flashy enough? Fine, use something else. That's what the repository is for anyway. The whole concept of TC isn't to have everything dressed to kill (or at least someone's peculiar interpretation of that; beauty is in the eye of the beholder) but to provide the bare essentials from which a user can build and customize to suit his or her own needs.