--check-roundabouts \
R 1 (and 7?) just do it and remove option. For the check options, I think there's a tradeoff between useful debugging and noise. So I wonder if by default there should be a file written (with a name derived from something) that has all the warnings, with each type having a unique first word, so one can grep out the ones one wants. Then they can perhaps just be on, maybe with a single option "--no-check" to skip the output. I don't see a lot of value in fine-grained warnings; getting the warnings that are the current consensus seems like the right thing, and I don't see a machine that is big enough to run mkgmap having trouble with the warnings file.
--add-pois-to-areas \
R 8. But could be considered to be just making it work in the Garmin format. Are there any downsides? The only downside is that if there is a node and an area, then you get two, but one could say that there are two in the source data, so that's ok. I think it belongs on, because otherwise POI-type things represented as areas vanish, index or not.
--index \
5 and 6. I'd be inclined not to make it the default I don't understand if the index code is stable enough, but I thought that generally people should want this. If that's off, though, it makes sense to default to off until such time as it's stable. Another usability comment is that I find the precompiled bounds situation a bit confusing. But maybe I haven't tried hard enough.