You are chasing a unicorn, as I'm sure you know.
I've now driven a 5 series with 6 speed MT for 13 years. Though the F10 does not quite approach the E39, it is, at least in the 550 version, an absolute delight. You know what you like to drive, so start the search.
I offer this advice only. If you find a car with the transmission that you desire, buy it. I passed on one in CA because I wasn't ready. It was a mistake. When the second one came available in Mass (with only 1,200 miles on it - long story), I jumped. That was two years ago and it was a marvelous decision. There are so few of these cars available, you really do need to be prepared to move quickly and have it shipped or travel.
Good luck! You are on the right track.
PS - One of 89 Carbon Black Metallic 550's with the MT!