But if I'm understanding correctly, it sounds like there's also a discrepancy between the Elektron synths and
other hardware synths; that's the bugger. Since all offsets and record compensation settings in SONAR apply universally to all I/O, there's no simple set-it-and-forget-it configuration setting that will address that.
Also we need to clarify whether we're talking about real-time playback sync or compensation of audio recorded from hardware synths, or both.
If it's only about playback sync, one workaround would be route all tracks and buses other than the Elektron stuff through a 'Delay' bus that delays them to be in sync with the delayed output from the Elektron synths (kind of like manual PDC). But, again, that's going to get awkward/complex fast, and cause problems with input monitoring latency while recording.
I would be inclined to work this issue with Elektron support.