Not sure about that.
One difference was that Blue Note payed the designated musical aggregations two days? rehearsal time. So the musicians were able to be more analytic and prepared perhaps.
Most Blue Note and Prestige sessions were recorded at Vangelders, although Vangelder says he had different recording set ups for BN and Prestige. He has said the differences were the result of paying attention to what each producer wanted to hear. Perhaps Vangelder himself preferred the Blue Note sound he achieved over the Prestige ones.
I think the song lengths are fairly consistent across both labels. Although BN might have favoured the 2/3 split and Prestige the 2/2 split.
Perhaps if it was more determined by personal and what material each musician bought to the session for consideration?
As between Prestige and Blue Note running times for LPs, generally Prestige seems to have had shorter albums. I've read somewhere (maybe here, or maybe in an MC sleeve note) that RVG advised Lion to aim for 18-22 mins per side. I think that's what was generally achieved. The only albums I can think of offhand that were quite a way below normal time were 'Hootin' 'n tootin'', side 1 of which was 16:32 (but side 2 just over 21 min). Side 2 of 'Drives' is 16:57, as well. But Prestige sides were often under 16 mins, some under 14 - 'Lonely avenue' 13:40, 'Hot barbecue' 12:32.
MG