Harry, yes, I think you understand this correctly regarding the options when creating captions from a transcript.
I found that once you open the preferences drop-down once, it will stay open for further caption creation as long as PR is open. The preset selected remains for further caption creation as long as the preset exists in the project that is open.
Having a default preset that can be selected is an important feature request.
Also, there appears to be NO setting that keeps the number of characters per line, etc. when creating captions.
Yes, there are MANY settings in the EGP that are not saved in the presets.