The Thracian theory is rejected by experts including Vermeer and Matzinger. Shkupi follows Albanian phonetic laws from the Latin just like Sharr, Shkodra, Drisht, Lezha, Shtip and possibly Nish and Lipjan because they have continiously been inhabited by Albanians since the Roman era and were preserved in the Albanian language. If they hadn't, the names known in Albanian would not be what they are today. Scupi would of not evolved to of become Shkup but in Albanian would rather be a Slavic loanword and so forth. The toponyms are a mixture of Slavic and Albanian due to Slavic-Albanian contact. The Bessi supposedly living in Dardania does not mean they were the proto-Albanians there were other main populations there and even the Thracian element there cannot be attributed only to the Bessi. The name Bessi came also to be applied to all Thracian groups. If Proto-Albanians had been the Bessi that means they picked up such toponyms including Nish and Shtip and Shkup and most in Albania from foreigners but thats not what the linguistic arguments suggest. They claim Nish and Shtip came directly from Albanian development, the Bessi did not originate in these areas which means the Bessi picked up such toponyms from foreigners. If such a theory was true, the placenames in Albania would show a different development too including Mat and many others.
Vermeer supports the transmission of Naiss > Nish and Astibos > Shtip yet rejects the Thracian theory for example or an origin from Thrace proper atleast. Matzinger rejects the Illyrian theory but says in some of his other works its related, Vermeer is unsure about the Illyrian theory but rejects the Thracian one. In Eastern Dardania there were definitely Illyrians that mixed with a Thracian one eventually which is what we will eventually see in genetics. I know Shkupi and Nish had a Thracian population. The E-V13 in Nish had a Thracian profile, something related to that.
Regardless, the Bessi theory is rejected by both Vermeer and Matzinger. They coud of not been proto-Albanians for various reasons. Matzinger supports the Messapic relation.