Looking at travelling from MAN to ABZ next summer. Previously when I've done this it has been solely domestic (so 1 hour check-in). Flights at the moment are only really showing via AMS with a reasonably short layover - 50 min or so (not enough time to e.g. exit and do anything sensible). Some times are also available via LHR but much longer. For these flights should I respect the international (2 hour) check-in window or the domestic one?
If you must choose such an indirect route then European (2 hours) it is, since you are proposing to leave the UK.
However, as mentioned in Comments, it seems there would be more direct, cheaper and quicker options than flying via AMS.
As an example for June 30, 2017, Flybe offer the following at present, amongst many other options: