When I put in the filters, they seem to apply to what routes that particular router generates only.
Correct, and that's exactly how it should be.
Example, I have a MT as a ABR between to areas, I only want to propagate some routes between the borders.
This can not be done
with OSPF filters. An OSPF router must never drop LSAs - doing so would potentially mess up the link state/topology calculation of other OSPF routers. It is allowed to be selective about which LSAs it installs into its own routing table (that would be the job of OSPF import filtering) or what external (i.e. non-OSPF-originated) routing information (such as static or connected routes) it considers to generate LSAs for in the first place (that - and only that - is the job of OSPF output filters).
Sorry, I'm used to cisco filters, and I'm assuming the MT filters should work like those.
Cisco does not filter received LSAs either, they also must (and do) propagate them.