Yes that is correct. When you make the LNX partition with HDDriver, easymint will call mkext2 (or how it's called) to write the ext2 filesystem on it. Don't worry about the cd-rom, I transfered the entire easymint installation with null modem. That hurts way more ;).
To install a cdrom drive on the atari, you need a program like metados, extendos or spin. These are cd rom drivers. There is also cd writting software, but to be honest I don't have a cd-rom drive so I don't know these stuff. Somebody else might be able to help. MiNT is great btw.