So if I optimise my main thumbnail for Mobile, it is then zoomed in cropped when viewing on Desktop.
Desktop and Mobile ratios are different? So you can't use the whole frame.
Yes, the thumbnail ratios are different depending on the device and browser/app. Etsy often change them without warning either whilst testing or just because they think it's better. Therefore I suggest making your first image square with the product in the center and a little space around the margins to allow for cropping either way. Subsequent images can be whatever you have already.