I'm trying to make a homebrew subrace combining the Eladrin (Variant) and Aereni High Elf subraces. I started by using the Eladrin (Variant) as a template, but when I try to create the 'Aereni Elf' racial trait and give it a modifier to grant twice proficiency, there is no option for 'Choose a Skill or Tool' in the modifier subtype drop-down. Oddly enough, if I do it the other way around and use Aereni High Elf as a template, the option is there for the 'Aereni Elf' trait, but if I modify it, the option disappears. Is there something I'm missing, or is the option itself missing from the menu? Is there a way to add modifier subtypes manually?

I've noticed there are a couple of hidden modifier choices that aren't readily available (in particular the rod of the pact keeper's warlock spell DC and warlock spell hit modifiers).

They are probably hidden to keep the already somewhat difficult to use homebrew tools from getting bogged down with all of the possible options. Or they just forgot to set them to be visible to public.

That might be a reasonable answer if the option "Choose a Dwarf Artisan's Tool" wasn't in the list, which seems a lot more niche!

I'm going to bring this back from the dead because it is still unnecessary issue. I should be able to give a choice of twice proficiency to a homebrew race.

You can, you just have to create a number of Options, one for each choice. So, for example, if you want to give them a choice between Perception or Insight, create two options, one of them would have Modifier: Twice Proficiency->Subtype: Perception, and the other would have Modifier: Twice Proficiency->Subtype: Insight. From the players’ perspective when making their selection they won’t be able to tell the difference.