Yea, Bio has a lot to do with it as @Hewjust stated.
My mace attack chain is, as mentioned, clobber, jawbreaker, shatter repeat. Those three are the highest DPA attacks in the set, so if you're using anything else, your overall DPS won't be as high.
Practiced Brawler is absolutely cutting into your time, but that just can't be helped. On my claws/sr(s), I keep hasten on auto and it's perma or dang near, so with its 2 minute duration, I use that as my guide to manually fire off PB so as not to waste end/time stacking it. The problem with just ignoring PB while pylon testing is that if you get hit, you're probably going to get knocked back, thus losing more time.
Other possible differences will be the incarnate choices and they DO make a difference. I go with Alpha Musculature Core, Interface Degenerative Core and Hybrid Assault Core. If you've got all three of those at T4, and the tightest chain you can get (which, granted, needs a ton of recharge but as you're SR, you should be able to get damn close to the 112% global recharge needed on top of hasten's 70% to get it perma,) then I'd honestly be surprised if you didn't end up under 3 mins, which is my claws/sr scrapper's average time. And yes, I DO always test with assault core toggled on to begin the test run because I always have it ready for hard target fights.
Total side note: I was amused that by pulling out my T4 Core Demon Lore pets (generally a no-no when testing pylons) BZB's time dropped from 3 mins to 1.25 mins.