Actually the difference you experience is not because of 4* purple parts instead of 5* blue parts - it is true you sometimes experience a PR drop after upgrading to another rank (common-uncommon-rare-epic-legendary) which has less stars, but it is 0-2 points only, so 4 upgrades make most likely something like 6 points difference. By that I mean: if you had 5* P911 with all 5* blue parts, its PR would most likely be higher than 662, but still less than 671. Or the other way round, if you "upgrade" that 4 parts on 993 to purple, its PR will drop from 671, but it would still be higher than 662.
So why is P993 better? Just a coincidence.
a) 993 is further in its upgrade cycle, you can get only one more star on a car and 2 rounds/upgrades for each part. On the other hand, you can get 2 more stars on 991 and 4 rounds/upgrades for each parts (not counting the conversion rare->epic and epic->legendary, as it does not add to PR)
b) each car have different span between its starting PR value and its cap when maxed out. P993 starts at 388 and can reach 758 (370 difference), while P991 starts at 508 and can reach 810 (just 302 difference). Both cars have similar upgrade possibilities (4 stageups of a car and 10 rebuilds per each part), which means that on 993 each stageup and part upgrade will create higher PR difference than similar step on 991. Yet 991 can have higher PR limit, so eventually it will surpass your 993.