Agreed, the worst that happens is that they say no.
Still, it’d be very unlikely at KLIA itself (others have mentioned more lenient practices in outstations).
MH603 is unlikely to be too late, so SK AAR shouldn’t worry too much on that.
Still, for ease of mind, I’d suggest checking with the Singapore forum, or email Changi airport directly, on whether transfer of bags at BR’s airside transit desk is possible, to have a clear idea on the chance that one would go to T3 airside and gets told ‘no’ there, and then have to backtrack to T2 to clear immigration and pick up bags personally, before again heading back to T3 landside.
(Just another point, EVA’s check-in appears to be open until 30mins before the flight, according to Changi’s site...)