The reason people did 64K alignment of bitplanes, and more often areas touched by the Blitter, was in order to squeeze out a little extra performance by not having to repeatedly set the high word of the pointers since it wouldn't change.
In a tight loop doing many smaller blits you could always up the number of bobs or whatever on the screen like this, especially on the unexpanded classic machines.
Aligning the data in your emulated Amiga on 64 byte boundaries to suit the outside machine isn't going to make a difference, there's just too much stuff happening for that to be noticable, but f.ex aligning your 32-bit accesses on 68020 and up will of course still matter inside your emulated Amiga.