He suggested a 46 stock as well, but after telling him I measured a bunch of jackets and the ones that fit better were closer to the 44, and that most off the rack smalls are too big for me, he said just go for 44 with 46 lengths. I'm just having that paranoia that first timers seem to have and kicking myself wondering if I should have listened to Charly, as is often repeated.
You can make a change up until the point where your jacket is going to get made, which will be a while from now. If it is as you say, then you should have no problem with the 44/46. To me, it sounds like the 44/46 will be a very slim fit, and the stock 46 would be comfortably roomy (not overly). If he didn't advise against it, you should be fine either way.