From the point of view of SIP and Asterisk, there is no difference between a “trunk” and an “extension”. (This isn’t about what FreePBX calls routes.)
The ways round it are to treat the “trunk” the same as the “extension” the same for matching, i.e. as an endpoint with a dynamic address, matched by the From user name, or to change the priority with which chan_pjsip matches user versus IP (endpoint_identify_order). I don’t know whether the latter can be done without breaking FreePBX in other ways.