It could be made but it would be still pretty custom biased - simply, there are tons of various HW options which can't be commanded by a 2-dimensional rule. There are a lot of exceptions which tends to became a rule. I can't see it happening.
New install script is less relevant as long as you have WHDLOAD.PREFS since it stores most common tooltypes/switches. As you said those are already present in individual game slave, but can also be edited to include some more.
AFAIK, people with WHDLOAD issues mainly report problems with a 040 compatibility which is a separate issue (decreasing issue in any aspect of WHDLOAD progress, for sure) and common, rookie footfalls of meeting minimum requirements (misspelling Kickstart RTB/KICK files, low RAM, poor's man 68000 etc). Issues like NMI or RESLOAD are less common since those cover HW banging or even issues with different WHDLOAD versions (so called KickEMU compilers etc.)
As you can see, issues exists, but they can be remedied.
Personally, I have around 100 WHDLOAD installs on my setup; maybe 5 of them had some problem which was sorted out after few forum searches, no big deal.
And all that comes with a HW which is known to be pretty dodgy with respect to operation (GVP A530 uses some not-so-great glue logic tricks for basic operations and that proved bad compared to other competitive designs. As a final outcome, I can't properly use SubWay USB on this config - board is a bad IRQ handler).