@media pdf {} is going to be interpreted only by PD4ML. So if you place the section after common CSS definitions, you may override them with PD4ML-specific ones.

Of course it does not help to solve “filter:” issue. In theory you may screen some CSS style sections (and avoid the parsing errors) under media types, not known to or ignored by PD4ML: tv, print, projection, handheld etc. But it is difficult to say if the major browsers ignore or interpret them.