It turns out that placing similar config files (i.e. bspwm-related) in
the same directory is not the way to go about handling dotfiles since
each config file (or dotfile) *should* manipulate only a single program.
This was not the case back when I used urxvt (which would require the
old method of .Xresources), but now that I understand more about how
*modern* dotfiles work (with $XDG_CONFIG_HOME), separating dotfiles by
program became the obvious choice.
Instead of "hiding" dotfiles in an extra group, it is easier to use
separate packages for each unique set of files. Since I'm working on
making my setup more modular, and since I can stow all my dotfiles with
a single command anyway, this configuration is more appealing now.
There are many dotfiles that we don't have to worry about when using a
desktop environment like Plasma or Xfce. These dotfiles are bspwm
specific and should all be stowed at the same time when stowing bspwm.