lr-atari800 issues are almost always challenges with quirks of the original hardware, especially the fact that there are many versions. This is where all the things like cart autodetect for 5200, dealing with alternate versions of the OS, dealing with BASIC or not, etc, all come from. You actually run into many of these on the actual original hardware too (the infamous "Translator disk" for example).
Basic stuff like controls is now pretty sorted, as of last year, except for the 5200's analog stick in a small handful of games.
This isn't to say that there aren't some emu issues -- there definitely are, especially with the slightly older version of the mu that Retroarch uses.
Things like Atari 5200 cart autodetect don't work reliably because the person who coded it originally tied the autodetect table to filename, for example. But given that there are many alternate dumps of ROMs with and without headers, even a checksoum solution would need to be pretty extensive.
I strongly suggest people who are interested in Atari 8 bit emulation take a look at the guides in my signature, and in particular use the script I wrote. It makes most everything pretty seamless on the computers, and walks you through building a 5200 library that just loads without fiddling with anything.
