I see two concerns:
- The given footprint is mirrored from convention. This is sneaky, because they give this drawing:
A cursory look might assume the pins are in the normal order, but the bottom drawing is the bottom view (hence the windings are visible inside the core). The land pattern is top-down, mirrored from this view.
You have a conventionally arranged footprint, which will swap primary and aux, causing poor and unexpected performance, or destruction.
In cases like this, I tend to ignore the numbering as given by the manufacturer, which is objectively wrong, and using a conventional pinout instead.
(It may be worth adding a note to this effect, to the schematic, or other design review materials, if other engineers will be looking at this and double-checking your work.)
In that case, you should change the schematic to have bias on pins 1-2, primary 4-5, and the secondary is in the same place, give or take phasing.
- You can swap all windings end for end, to get the same response; at least at low frequencies.
At high frequencies, it may be preferred to keep one or another end of a winding near GND, or referenced to certain ends of other windings (typically VCC and GND, both being AC-ground nodes), and then the choice of which end to ground matters, or which end of the winding the rectifier diode goes on. (With a sync rect, I think this probably isn't applicable here, but to say there are cases when it is.)
For such a small transformer, and at low to moderate voltages, this probably doesn't make a difference. It may also be that the transformer isn't made with the particular winding techniques, or shielding, where this would affect the result (in other words: don't worry about it).
It's also a "don't worry" situation if you won't be re-doing the design, to optimize transformer windup, component placement, EMI filtering, etc. Since, you'll do the design, the EMI filtering is whatever it needs to be, and that's that; maybe it could be simpler if a more suitable transformer wiring or windup were chosen, but if these aren't variables you're going to test, then the EMI is just whatever you get with the configuration you will test.
Assuming of course, that EMI is a concern and will be tested.