Good question.
Indexing multiple tokens at the same position is a very reasonable idea--if not else, to index variants of the same word. There is nothing in MG4J that prevents this from happening--the only problem is that there is no support in Scan for this.
There are way to patch the problem--you can, for instance, break the multiple annotations in a small number of different indices, and then just merge them. Like, one index has
> position token profession ....
> 1 Rembrandt printmaker
> 2 was
and the other
> position token profession ....
> 1 Rembrandt painter
> 2 was
The resulting indices would have disjoint term sets, and if you merge them you'll get what you want.
Probably the best thing would be to have a new type of field, ANNO, that returns a position and a token (in monotonically nondecreasing order). The indexing system that would just index the token in the right position. If you're interested I can try to put it together.
Of course, you have the possibility of building your own index using a suitable IndexWriter--it's quite easy.
Ciao,
seba