Drush make and multisite
By checking the drush code itself, we discovered the possibility to add contrib_destination on specific project level.

projects[views][] = ""
projects[views][contrib_destination] = "sites/site1"


However, as it would had quite a lot of lines to the makefile (we must add the contrib_destination line to all modules used by site1 only) we decided to not use the includes feature and to keep to separate makefiles.

To build our docroot, we then have one "global" makefile to prepare the sites/all modules and another ones for each subsites (sites/site1). Then we launch the drush make command for each makefile (using a shell wrapper to handle it).

This is not perfect and would probably be easier to have something build-in (I don't know what would be the best syntax for that).