Accents over lowercase are positioned horizontally; accents over Uppercase are positioned both horizontally and vertically.
The reasons why yours move up over Petite Capitals and mine do not is due to different versions of UnicodeData.txt
I reported this to Erwin to see if it’s a bug not to include the modified UnicodeData.txt in a standard installation. (Edit: I searched the Beta forum and found that it was intentional to include only the standard UnicodeData.txt file from Unicoode.org. This file is updated for each Unicode version update to add definitions for new glyphs, or include other changes).
As a permanent solution, I suggested deleting the AppData version of UnicodeData.txt if you have one and saving the version from the linked thread in AppData\FontCreator\Unicode. That UnicodeData.txt file defines Petite Capitals as lowercase. The modified Blocks.txt file simplifies the Insert Character dialogue if you don’t use CJK etc.
The easy solution that you alluded to is to temporarily edit CapsHeight to equal x-height before inserting the Petite Capitals with the Transform script. Then recalculate the metrics afterwards.
Later versions of FontCreator include Unmapped Transform scripts. Since they use no code-points, some problems like the above are avoided. However, the unmapped glyphs can only be used by applications that support the relevant OpenType features.
All of this information is documented already (mostly by me), but I admit that it is hard to find it. Over the years I have provided a lot of free support, but I use the software much less frequently now as I now have all the fonts that I need. I test each new version of FontCreator and update my own fonts when bugs are found.