Just to try to clear some of the confusion with the dictionary definitions...
[De rapaz, mas de formação obsc.]
- P. us. no Brasil Mulher nova; moça: [...]
- P. us. no Brasil Adolescente do sexo feminino.
- Lus. Moça do campo
- Bras. N. N.E. MG GO Amante² (6) ou concubina.
- Bras. N. N.E. MG GO Meretriz. [...]
- Mulher nova. =JOVEM, MOÇA
- Mulher entre a infância e a adolescência. = MOÇA
- Menina pequena.
- [Brasil] Meretriz.
It appears that according to the ptPT dictionary Priberam, the pejorative usage is restricted to Brazil. (The Dicionário do Aurélio you link to is based on the ptPT Dicionário Priberam and not on the ptBR Dicionário Aurélio.)
Moreover, the ptBR dictionary Aurélio is more precise about where in Brazil rapariga is used pejoratively: primarily in the North (AC, AP, AM, PA, RO, RR, TO) and North-East (AL, BA, CE, MA, PB, PE, PI, RN, SE) regions, together with the states of Minas Gerais (MG) and Goiás (GO). That is, here:
(image adapted from SVG file on Wikimedia)
In other areas of Brazil it can also be used to mean "young woman" or "female adolescent", but this usage is rare (P. us. no Brasil = Pouco usado no Brasil).
Does “rapariga” have a pejorative connotation in ptPT?
No, rapariga does not have a pejorative connotation in ptPT.
ps - Even though "meretriz" comes as number 4 definition in "Aurelio Online", I always heard it as a pejorative.
This online dictionary "Dicionário do Aurélio" doesn't have anything to do with Aurélio, but is likely based on the ptPT dictionary "Priberam", so one shouldn't expect it to give definitions pertaining to Brazilian Portuguese.