Why does poleepodium sound right?

This is an accurate transcription of the first two syllables. The vowel in poly is a long ee in ordinary speech, and ee is the plain English way of writing that sound. The spelling refuses to record it, in this word and in polyester and polythene and polygamy, because the y is doing historical work rather than phonetic work. It marks the prefix as the Greek one.

Two separate decisions about the letters, both made at once.