Sound from disk can overlap with the boot logo. For me, with two drives, TTSClock normally overlaps frames 50 or so onwards of my boot animation. It does depend entirely on your hardware (in particular, what kind of drives you have and how long they take to respond). You certainly can't expect to synchronize sound and vision.

With a long animation, you have to take care with its size. JEmplode won't upload anything longer than (I think) 64 frames in length (regardless of how many distinct frames there are). I recommend making a boot animation that repeats frames, keeping the number of distinct ones down to a minimum. You'll need to use Mark Lord's aniwrite on the player, or use some other means to upload a long animation that JEmplode refuses.

Alternatively, with some kernel hacking, you could probably do a simple tone-generator to do simple tunes (probably of similar complexity to a mobile phone ring-tone) from flash.