Turned out I could solve this without api change.
Well, I "cheated" of course by writing a new MultiFileChecksumHelper instead of modifying the (single file) ChecksumHelper class.
Anyway, this issue is now fixed.
And: not only is jetspeed-portlet.xml now properly checked, but I also throwed web.xml into the mix.
As some registry info is retrieved from web.xml re-registration should also be done if those change.
Please note: as the current checksum is stored in the database and this fix will lead to a completely different checksum,
all existing deployed portlet applications will be re-registered once.