Create phantom parts/assemblies like in Inventor/Solidworks?

‌From what I understand of phantom parts and their use in Inventor and Solidworks and how the created the equivalent is done using Windchill. I haven't used it so I don't know the details of getting it to work. Doing a search turned up a link to Windchill Phantom Assembly Infrastructure which as I understand it is what you're looking for. It's only an overview of the Windchill functionality and use but it's a starting point.

I looked this up - https://knowledge.autodesk.com/support/inventor-products/learn-explore/caas/CloudHelp/cloudhelp/2014/ENU/Inventor/files/GUID-A0A95805-CBF6-4524-8314-4AC8B53C19CF-htm.html

Hard to see a replacement in Creo/Windchill as it seems like Autodesk is trying to embed a PDM into Inventor.

Are you creating you BOM's in Windchill PDMLink, or on Creo drawings via tables with repeat regions?

If you're using PDMLink you're in luck.  What you describe as "phantom parts", sounds like what PDMLink calls "gathering parts".  Create the WT Part records as normal, based on your CAD hierarchy.  Edit the WT Parts for the phantoms and change the "Gathering part" toggle to "yes".  They will take on a special icon, and will not show up in BOM reports for items they're placed in.  Instead, their contents will appear in the report, as if they were directly in the parent.

In case you or anyone else is confused...  PDMLink is actually CAD agnostic; it's designed to also work with CATIA, etc. So the BOM reports aren’t directly based on CAD hierarchy.  CAD models get associated to 'Part' records which hold all the metadata (we informally call these records "WT Parts" as the word "part" is too ambiguous in conversation).  You can even have various CAD Parts linked to the same WT Part, if there are models of the same thing in different states.  If all goes well, checking in CAD models will update the hierarchy of associated WT Parts.

We had a 3rd party vendor create a tool to create PDFs of BOMs that match a legacy company format. Unfortunately, it doesn't respect the "gathering part" toggle, so we can't take advantage of this feature. I'd like to get it supported, as I see a few use cases where this could be really handy to stay organized, but it's seen as a low priority.

I haven't done much with repeat regions, and never create a BOM with one, so I can't offer specific advice if you're putting BOMs on the face of drawings..  But, I'd investigate the filters.  Maybe the BOM by default could include everything in the current level, plus one level down.  A filter removes any item that has parameter "phantom_part=yes", or any item who's parent has "phantom_part=no".  (Just and thought; no idea if it's viable.)

Good luck.