It's just like a rental, you can have as many names as you want.
As Gareth said, you will lose the first home buyers, which honestly isn't "really" a problem.
To then quality for it you would need to purchase another place, move into it etc (or fake it, and have someone staying there off-books, another risk).
Basically getting a 1st Home Buyers grant (for you both, over 2 places) isn't going to happen unless you dodge it up in the short term.
So what you would also do as part of the agreement, is split the "value" of the FHB between the two of you as you are both effectively giving up your eligebility.
He could argue he wants full value due to him supplying the deposit but that's something you'll need to workout between yourselves.
Issue down the track there after you need to then think about is furnishings and what not. Again it can get "petty" if things go sour in a few years time with regards to who owns what, who brought what to the house etc.
Same goes for any spending on property improvement and so on.
Sounds like a mine field, but approached logically and everyone keeps honest records - it should be straight forward