If Jude understood Michael and Jesus were the same, would he not have referenced that important point?
According to Origen, the writer of Jude was quoting the Assumption of Moses (1rstcentury CE). We are missing about 1/3 of that so it's possible it was within that section. Others believe he was referring to a composition that included the Assumption and the Apocalypse of Moses (wherein Michael is driving God Most High's cherub-pulled chariot carrying the bodies of Adam and Abel to be buried in Eden which has been relocated to the 3rd heaven). This gives Michael the role that would explain the Jude passage where Satan demands Michael reveal the location of Moses' body.
The writer of Jude may been in fact combining that tradition with the Zechariah scene above. Many regarded that pericope as proof of a second power, the angel of the Lord, that acts and speaks as the Lord and seems to be acting on behalf of the 'Almighty' to war with enemies. In short there was a diversity of terms and roles assigned for emanations of God. Some of it appears by design others may have been artifacts of translating.
It would be far too much to expect every writer to share identical imagery and conceptualization of the Great Prince Michael/Angel of the Lord/Son/Logos. You are struggling because you are mistaking these allegorical stories as literal and frustrated that they are not consistent in detail.