from the looks of it the XI strut is quite a bit different, I only looked at stock photos online, but I do see the 2 dots your referring to. the 335i RWD models do not have the 2 dots, but they do however have a small tab that stops the strut from going further into the clevis and also probably use for alightment as well as there is a mark on the clevis to match it to. cutting approx. 1/2" off the strut alightment tab shouldn't be a problem, and will still leave enough that is welded on to not be an issue, look at photo below for more detail.
It also looks like the XI strut taper is much more extreme and made to do exactly like you said, keep it from going any lower and hit the front drive shaft. the RWD model has a much less extreme taper, and from photo I have seen the taper actually already goes through the strut clevis on the bottom so there is nothing stopping it from dropping further into the clevis other then the tab on the top.
Regardless, I will still make sure I take a good look at it prior to cutting the tab, I will likely only cut the tab to flat, or IE remove the bottom section where it floats not welded onto the strut, maybe a little less than 1/2" but still something is better than nothing.
335i RWD
f30 suspension, but should be similar...
XI front strut
