Current, lirc's autotools configure script will use libftdi and portaudio if they're available. There should be options to not use them even if they are available - there should configure switches named (perhaps) --disable-libftdi and --disable-portaudio.
Lirc already has similar options such as --enable-devinput
See https://bugs.gentoo.org/663680 for the problem this is causing in Gentoo.
This problem was caused by https://sourceforge.net/p/lirc/git/ci/81a55d23049b7153207a943b3a7c890ca574c686 (before that commit, drivers could be individually enabled/disabled, now they're automatic based on what libraries are detected - we really need library dependencies to be explicitly enabled/disable if they're optional so we don't have automagic dependencies)
I agree with your description of the problem, but I do not agree with your solution.
The basic problem is that the Lirc distribution contains a lot of "cruft": non-essential drivers ("plugins") for often antique or obsolete hardware, with no known maintainer. Whether there is any active user is also unclear. The maintainer can check that they compiles, but not if they work. And they "contaminate" the Makefile with all their options. The purpose of Alec's commit was probably to clean this somewhat -- but he left the drivers/plugins in-tree.
Thanx to the new plugin concept, these can now be handled outside of the main source tree, and built independently.
What I would propose is to move all the "non-essential" (to be determined what this means) to a directory contributed/plugins, each of the drivers/plugins in its own directory and its own Makefile.
(Like in the X11 distribution from MIT/X Consortium.)
Alec?
BTW, I am a strong proponent of "positive logic". I think --enable-foo is to be preferred over --disable-foo, regardless of the default (which can change).