4.1 SP4 MR3 = 4.1.4 MR3 (Rollup) (Bundle 131)
4.1 SP4 MR2 = 4.1.4 MR2 (Rollup) (Bundle 111)
4.1 SP4 GOLD = 4.1.4 (Bundle 24)
4.1 SP3 GOLD = 4.1.3 (Bundle 37)
I followed the directions you listed above, and my BES identifies as 4.1.3 (Bundle 37). The problem with this and your list is that our mail server is Exchange 2003 as part of Small Business Server 2003. BES is running on a stand alone version of Windows Server 2003 R2.
We do not have Domino installed anywhere and never have.
BES was installed back in July 2007 (BES Express as we are only using 9 licenses at the moment). As it has been running error free since, and I had other issues to face as the new (and first ever) network admin for this small but growing business, I haven't tried to run any updates on it. Now that I've settled into the job, I am finally working on getting this up to date.