Well, look at it this way... If you intentionally choose to not
install that piece, then you choose to break things that might depend
on it. So yes, you have that choice, but there are consequences for it.
I don't know what else you would also potentially break, but it's easy
enough to simply put in the requirements of your software program that
you require the BSD subsystem be installed. I'd liken the 'optional'
but here to also say that printer drivers are optional, and you don't
have to install them... Now, is it up to the application developer to
figure out that you didn't and somehow work around that? Maybe a far
stretch, but similar in the vein that the user took some intentional
action to remove a part of the standard install.

Now, if this were a company product where real money was being charged
for it and there were a compelling reason to make it as idiot proof as
possible, despite what the users may have done to their system, then
I'd agree with you and would be compelled to try to make it work.
However, that is not the case, and there are design decisions to use
the base or common denominator of a standard set of components on top
of a standard install of the operating system with it's default
options. Just my opinion, anyway.

I'm not intimately familiar with Python, this is the first time I've
worked with it. However, after discussing things on the PythonMac
mailing list, it came out that bundlebuilder.py was the way to generate
a bundle. It doesn't mean it's the best, or the most fool-proof, etc...
So the options are possibly open for an alternative, nobody can be
aware of every alternative way to do something, no more than they can
know every conceivable end-user configuration they'll be running
against. If they could, I suppose we'd have no bugs or errors in
shipping code. :-)
Always open here, I don't claim to have any lock on the best way to do
things (if there is one, opinions abound...) and can always learn
something new and useful.