As you are talking about topolectal dictionaries, which are not based on the ISO that Hànyǔ Pīnyīn has, there is no single standard. The ISO standard for Hànyǔ Pīnyīn of course just appends the -r, without visually indicating any vowel or nasal consonant changes, just as the standard also rules against visually indicating the tone sandhi in consecutive tone three syllables.
I would presume as a trend though that phonological adaptations are useful in a topolect dictionary, and so any one that uses an orthography based on notating the sound (whether it is a custom romanisation system or an IPA-based system) would try to present sound changes in the surface representation and not only the underlying morpheme structure. Hence the unrounding of -o to -e in 头儿 that you see.
For more complicated instances of vowel change, I think it's pretty much required. Fuzhounese, as one of the varieties of Chinese that has morpho-semantically-motivated vowel tensing, really needs the vowel changes to be notated.