There isn't currently a way to sync scroll positions of two file displays, sorry. (It would probably also need to add gaps where a file on one side is missing from the other.)
We may expand the Synchronize tool (and also Navigation Lock, which could benefit from this idea as well) in the future, but if you need this kind of functionality now, I'd recommend integrating a dedicated diff/merge tool into Opus. WinMerge is a good, free option. Beyond Compare is a very good, inexpensive option and what I use personally. (There are lots of others, of course.) Both can be easily integrated into Opus so that you can launch them at the click of a button to compare files of entire folder trees across two file displays:
[ul][li]"Smart" front end for Beyond Compare[/li]
[li]External Compare and Merge Tools[/li][/ul]