-ii is from when they Latinized the author’s name as well. So if it’s called thomasii it’s because Thomas was latinized to Thomasius, then with the possessive replacing the suffix it becomes thomasii. -i is when the root is the unlatinized name (which personally I prefer, I’d rather minimize the effects of obscure Latin rules of grammar, gender, etc. in nomenclature).
I’ve never heard it pronounced with a glottal stop, only with then gliding together like the ea in “keala” in Hawaiian. To the extent there’s a separation it’s more like a y sound between, like ee-yee or ee-yī.