FS still needs to see the signalling to start up the call.
You'll need to bridge the call from the Windows FS to the Linux FS, and then have Linux FS send the call on to the final destination either directly or via the Windows FS by bridging back to it (but on another profile/dialplan/extension so it knows it's to send out to the phone not to the Linux FS).
Client ----(g711)----> Windows FS ----(g711)-----> Linux FS ----(g729)----> IP Phone
Client ----(g711)----> Windows FS ----(g711)-----> Linux FS ----(g729)----> Windows FS ----(g729)----> IP Phone
Directly from Linux FS to phone would be optimal, but you'll need to do it via the Windows FS if you're using the registration data to know where to send the call to.
Using bypass_media would allow you to avoid sending media via Windows FS which'll massively reduce the server load. SIP signalling uses hardly any CPU since there are very few messages during most calls. You'll get the following paths:
Signalling: Client ----> Windows FS ----> Linux FS ----> Windows FS ----> IP Phone
Media: Client ----(g711)----> Linux FS ----(g729)----> IP Phone
-Steve
.