Also, “not having a known etymology” is weak evidence for borrowing, full stop, let alone for borrowing from a substrate. There are lots of very common words in english (dog, pig, boy, girl) that have no known etymology which are incredibly unlikely to impossible to have come from a substrate language.
Languages invent new words and sound patterns endogenously all the time.
English dog has had an etymology for the last 20 years or so (Gasiorowski's) that many find convincing. But with regard to Greek lexicon, it is not just the lack of etymology that suggests substrate but the non-IE phonology of many of these words.
Languages invent new words and sound patterns endogenously all the time.