Okay, so sounds like you're looking for a way to manage the alignment of the physical part when you assemble the real PCB?
To start with, I would create a PCB footprint for the module, including the 3D model and some 2D reference geometry (on the 3D Body layer or just on an additional mechanical layer). You can include a silkscreen outline to visually align the part to when assembling, depending on the overall assembly style that might be good enough. Make sure the silkscreen marks are very close to the edges of the module, if the edges of the module land on the silkscreen lines that will probably be best.
If that's not good enough, you could add holes to the PCB footprint for dowel pins to align the module. You'd want three pins: two on one side of the module, and one on an adjacent side, near three of the four corners. Sketch attached. Push the module down against the two pins and then left against the third pin, and that will get pretty good alignment of the module on the left and bottom edges. Once the module is fixed in place, you can pull the pins out. The holes should be a fairly close fit to the pins. Or, you could build an alignment jig that holds the module in place while soldering. Jig could be 3D printed, laser cut, built up from PCB scraps, or whatever.
I'm a little skeptical of soldering one corner of a module like this. Unless the edges of the module's baseplate are solderable you'll need a layer of solder between the module baseplate and the copper of the PCB, which could make the module sit unevenly, or even stress the PCB if the module is clamped down tightly. If you keep the solder mask intact under the rest of the baseplate that might give enough of a gap between the module and the pad to allow for a bit of solder. Adding silkscreen to the area under the module would increase that gap and might be better. Both of these would reduce increase the thermal resistance between the module and the PCB though, which might be an issue for you?