That's works for me too... then a robot is built once the assembly is complete. The problem seems to be inside the code of the assembler. My gut is telling me the assembler is checking the archetype of the base species (BIOLOGICAL) rather than the class of the actual species (ROBOT) and defaults to building the first robot it finds.
ETA: My most recent game I went so far as to remove all robots and robot designs from my empire once I had ascended. Then I gave my species a trait and changed the whole population to match. Then I force-locked all assemblers on my modded ascended species. The assembler built unmodded robots and I had a new unmodded robot design under my species tab.
Ah, ok, so thats some good information.
So, I was able to reproduce your problem.
I was also able to succesfully create Ascended Synth Pops by janking around with the Select Species UI. Literally repeatedly clicking around species selection allowed me to correctly select and build my Ascended Synth template.
That actually probably narrows down the problem quite a bit, and my guess tells us that its a UI issue.
This kind of issue seems similar to other UI issues where you have two different windows competing for the same z-axis position. It would make sense if Ascended Synths were generating an extra(blank) select species window in the same position and z-axis.
Try reproducing that. Once your planet has an Ascended Synth pop on it it should show up in Select Species. The little checkmark icon ("selected_icon") isnt showing up for me, but by clicking around the window for my Synth Species ("planet_species_select_entry_specific_species") I'm able to lock it in as the species im assembling. And yes, whats popping out the other end once assembly is complete is the Ascended Synth, not a robot.
Edit: I'm finding the above issue to be very reproducible. If you edit your Ascended Synth species to have a different portrait than your robots, then it becomes very obvious when clicking around on your Select Species panel actually locks your Synth in as the pop being assembled.
Also, I dont know if its working the same for everyone else, but I'm totally able to select my Ascended Synth species for assembly up until I've completed the special project to modify their species to have some traits.
IMO the source of the UI issue here is possibly related to all the issues other people are having when gene editing their Psionics or Driven Assimilator Cyborg founder species.