The new Glyphs manual states
You do not need to anchor a node if it is going to be the origin of a Stem hint, because Glyphs will automatically (and invisibly) insert an Anchor instruction.
but this is not always a good solution. Sometimes you want to add a stem without any anchors, even if it is close to or inside an alignment zone.
Hmm. I do understand, because a stem is not allowed to start without an anchor or piggybacking on another instruction, but I feel uncomfortable not seeing what is happening. What if I wanted that anchor not locked to the alignment zone?
Then you can select the no stem or interpolate options.
If your manual is correct, defining a stem automatically sets its starting point as an anchor aligned to the nearest pixel edge. Changing the alignment of that anchor has absolutely nothing do to with interpolations or not rounding the stem to a control value. How come I always get an answer to a question I didn’t ask here? 
Is it possible to change the alignment of the anchor?