Outside of interference with the hub or spokes, which should be immediately obvious, I don't see any reason why you couldn't do this. Be aware that if you insert bolts from the inside that if they loosen they will also move inwards potentially fouling the wheeel; keep an eye on them. Another alternative would be to use "P-clamps" on the seat or chain stays to mount the rack and fenders, like would be done if there were no dropout holes. This site: http://www.bikebagshop.com/rack-accessories-c-89.html
has some accessories for rack mounting; a search on "bike rack stay extenders" will yield more.