The Fire Stick runs the Android Plex client, and supports a large number of formats. The general rule is going to be: don’t use HD audio formats. But AAC, AC3, E-AC3, FLAC, and Opus are all fine. HEVC is fine for video (I assume this is a fairly recent Fire Stick). You can leave the subtitles in the original PGS format they are on the disc, too.
MKV is a container format for enclosing all the parts of the movie (video, audio, subtitles) into one file. Honestly a “correct” MP4 file has some strict rules about what can be in it, so you do want to use MKV for your ripping really.