Yes you can set your interface MTU at 9000 and assign a 1500 MTU to the routes themselves.

> […] and assign a 1500 MTU to the routes themselves.

See "mtu" option in ip-route(8):

* https://man.archlinux.org/man/ip-route.8.en#mtu

The BSDs also have an "-mtu" option in route(8):

* https://man.freebsd.org/cgi/man.cgi?route(8)

* https://man.openbsd.org/route