Hey, i ran into the same issue and your post was really helpful, however when you explained that you can offset the matte in fusion, i just couldnt find this option. After a bit of trying out different things, i think i found an even quicker workaround, since the matte and the original clip perfectly aligned on the timeline and only were off in fusion and the color tab due to the original clip being trimmed at the beginning, when i selected both the original clip and the alpha matte aligned perfectly on my timeline and made a fusion clip out of them, the timing was already matched up and all i had to do was reconnect the matte clip as alpha for the original (+delete all the merge and background nodes resolve added when the fusion clip was created). No fiddling around with the Offset option as you mentioned