The usual way for 68000 is as you say to store unsigned shorts in x86 format and xor the address with 1 when reading bytes.

For the 68020 the process is the same but store unsigned longs and xor address with 2 when reading words and with 3 when reading bytes.

Unaligned reads aren't that hard, there are only three cases. You just do two reads and shift each value, like the real chip does. In terms of emulating an Amiga, that is easy.

smf