This question was answered on the mod teams discord, but I'll give the answer here for consistency sake and in case anyone else is curious.

Unlike most other units, ships like the PDF and Carrier DHC are in a unique place, since they're technically buildable in Era 1 FTGU rather than progressives, so most of the work has already been done.

To make the two ships buildable, you need to navigate to Data\Scripts\Library\eawx-states\tech, then open files named tech-era-two through to five. Within these files, either delete or comment out (-- preceding the entry) the mentions of the PDF_DHC

This process allows you to build era 1 republic units like Republic Troopers and A4 Juggernauts, as well as unlocking units that lock mid game (Acclamators, TX-130s). This also applies to the CIS, but they have fewer locks/unlocks than the Republic,