1) You might still be able to find a GBA sized 3 in 1 to work with the DS and a DS flash cart, technically it will work on a GBA as well (well all of one game at a time) but it really does want a DS/DS lite to work with. Otherwise yeah it is the only one still made by the EZTeam, and in fact is the only cart still available in shops that is worth purchasing (your other options are mainly old GBA supercards, fire cards and clones thereof and stuff a shop might have found in the back of the warehouse, none of said options a good choices really).
The EZ4 is also a standalone flash cart -- it has a microSD these days (older versions used the quite difficult to find miniSD format) and you patch GBA ROMs however you want (the EZTeam provide EZ4client for this) and transfer them to the ?SD card. You might be able to do something with the linker but 99.9% of EZ4 owners run it standalone.
2) Yeah it is real time clock. As the GBA did not have a clock chip in it (like the DS and most things since) it needed an extra chip to do it. For the most part it only really troubles fans of pokemon, though there are patches so that clock advances during play time.
http://gbatemp.net/threads/buying-a-gba-flash-cart-in-2013.341203/page-18#post-4756995 has more on the various trouble games and what can be done to fix them.
3) Yeah GBAATM hardpatches cheats into GBA ROMs, though if you want it does have cheat enable/disable options.
4) Mainly because you need to install drivers and later versions of windows got odd there (signed drivers being required, 64 bit versions of windows...). Virtualbox these days has great USB passthrough support so you can use that instead if you want.