I don't remember those clearly. My most clear memory of an Afarsek is from Kesuvos 112a. There it seems to make more sense for it to be a fruit.
Over Shabbos I found Kilayim (first perek), where a shaked and afarsek are listed as "kilayim zeh bazeh." Pirushim on the page struggle regarding what the chiddush was. I had assumed due to the similarity between an unpeeled almond and a peach pit.
Tzedah Laderech (in Miketz) says it is mistaber that botnim are pistachios and not afarsekim because "we don't find that we make shemen from afarsekim," and the midrash (I found it in Targum Yonasan) translates "mishach dibutnin."
Lastly, in Eruvin the Gemara wants to know why the shiur (mazon shtei seudos) for afarsekim (five) is not the same as the shiur for tapuchim. My mistake was from there, because the shiur is listed right after shkedim. But the one after afarsek is rimon so not a proof either way. Same with Maasros 1:2. But there are other Misnayos where "parskin" are listed with just fruit. There are also places where it is buried in nuts (Shabbos 21a, gemara).
The Bartenura (Shviis 7:5) translates 'bitnah' as 'pistok' (as does the Rambam) and says it comes from 'botnim ushkedim' in our posuk. In Pesachim 10:3 he says that charoses is made of "מתאנים ולוזים ובטנים ושקדים וכמה מיני פירות ומשימין בה תפוחים". At that point it shouldn't be surprising that he lists nuts with botnim in the middle - after all, they are pistachios.
So probably both botnim (which are haetz, whatever they are) are wrong and afarsekim might also be (based on the first source) but the pirushim there seem to hold it is a fruit.
Glad I looked them up and got it straight in my head. I've seen more but this is what I was able to find unaided.
