I found this thread because I am suffering the same issue. My first experience of this issue is when I created a pump as custom equipment and I kind of found a work around, Keep in mind that I developed this work around while creating custom equipment from an existing 3D model. I'm not very experienced with P3D so I can't speak to how this would work with the supports or components in a catalog or spec which I think most people call those things parts.
Anyhow....I have my 3D solid body model of the pump. I turned the 3d solid body model pump into a block. Which you need to do anyhow to create a custom equipment. Once I had the pump block I draw various objects on top of the block (lines, polylines, points and circles) as reference geometry. I draw this reference geometry to represent the various points of references I will need for the pump such as the center of a nozzle, face of nozzle, bottom center of base, center of pump housing, back center of motor, all (4) corners of base plate, etc. I then select all this reference geometry I create and turn it into a block and this block is sitting perfectly over top of the equipment model. I then add my nozzles and I use this reference geometry block to specify center of nozzle and nozzle direction. Now as you may know after you add a nozzle and now you have an equipment with a nozzle or nozzles, you can snap to that nozzle center while using commands line move, copy and measure. So what I do is add nozzles to various points on my reference geometry. They're bogus nozzles and not nozzles at all really, but it gives me a snap point when I need to measure to the back of the motor, or to the bottom center of the base plate and other things. For good measure I keep this reference geometry block with the equipment by using the PLANTEQUIPMENTATTACH command to attach the reference geometry block to the equipment. Now once you attached reference geometry block to the equipment the objects in the block cannot be snapped to because it's equipment, but you do have your fake nozzles set up to be used as snap points and the reference geometry block you create is attached to the equipment. If you every wanted to add another nozzle to be used as a snap point you could use the PLANTEQUIPMENTDETACH command where you would detach the reference geometry block from the equipment (temporarily), use it to add nozzles and also if you needed to edit your reference geometry block to add more points of reference you could do that and then when you got it all set up like you want go ahead and attach your reference geometry block back to your equipment by using the PLANTEQUIPMENTATTACH command again.
Here's a screen shot of the pump. I have a nozzle set up for my suction and discharge ports, but I also set up a nozzle N-3 as a snap point for the bottom center of (1) side of the pump base plate.

I guess the down side is a bunch of nozzles on the equipment that aren't really needed as nozzles. I'm new to P3D so I don't know how this would effect P3D functionallity relative to catalogues, specs, orthographics, isometrics and P&ID.
Thanks - Mike