There is no Merge function, but Synchronise (SmartSync profile) default settings should copy files on X that don't exist on Y (and vice versa). For files that exist on both sides, you have to make your own rules/decisions. Bear in mind that Decisions-Files settings (rules) that rely on 'previous-state' being known (which presumably won't apply to you) simply won't trigger.
For example, a rule that says 'if file deleted on X but changed on Y since last-run' simply won't trigger on run-1, because it has no idea there ever was a file on X (all it knows on run-1 is, it's not there) or that it has been changed on Y (all it knows is its state now). But you can set 'same file (name) on both sides' to 'pick newer file' OK. You may need to monitor the Differences window and be prepared to 'intervene'
For example, a rule that says 'if file deleted on X but changed on Y since last-run' simply won't trigger on run-1, because it has no idea there ever was a file on X (all it knows on run-1 is, it's not there) or that it has been changed on Y (all it knows is its state now). But you can set 'same file (name) on both sides' to 'pick newer file' OK. You may need to monitor the Differences window and be prepared to 'intervene'