[...]
[NOTE: the actual reason I am telling all of this is that I would like to know if there are better ways of solving the issue ...]
I guess I don't really know all of the story, but I simply wonder why you distribute the pre-built docs at all? Why not have them built, just like all the other stuff? To me it seems that building the documentation takes quite some time, but the checks take even more, so why bother?
One other note (I'm not sure whether this still applies to pre36, it was true as of pre35): You overwrite the all target of doc/Makefile by a no-op, which is inconsistent with the other targets, which have their usual meaning. To some extent, it makes sense because you intoduce more targets (like user-configured, etc.). But wouldn't it also be an option to just remove doc from the SUBDIRS entry in the top-level Makefile.am and have users always do the stuff manually in doc/? Which, of course, means that we need to run make -C doc clean, make -C doc install, etc. Just an idea.
Best, Michael