The Pillager bonus is only 5 points, not 10, and it’s for breaking 90% of Ashen Phyacteries. Your 100 points for completion is hardly affected if you miss a single pot on one floor (maybe you’d get 99 points instead of 100).
Where did you get the idea that you’d lose 10 points? Also, you can literally ignore the timer as long as you get near 100% completion and methodically work towards 60-65 bonus points -OR- you can gogogo.
I got a 5-gem score on my second run with only 86% completion and it still took me 24+ minutes. It’d be nice if Blizzard explained the scoring with an in-game sign in the Torghast lobby, but at least do some research on Wowhead because it’s not hard to score well (if you care about that). It definitely is harder to unlock the next layer than it used to be though (used to get 5 free deaths and now that would cost you -100 points).