Still in nuendo 12 but

Do we know if in nuendo 13 the Order 7-1-4 is correct?

This is still the case in Nuendo 13 as well:

In Nuendo, the order of surround channels and side channels follows the specification of Microsoft Inc. To meet the Dolby requirements for side surround channels and surround rear channels, swap the device ports of the surround channels and the side channels.

Basically, things are a bit confusing. In the audio connections, the order of the speakers at the inputs may be different from those at the outputs. (With the same channel configuration, mind you.) But if you pay attention to the correct assignment, this should not be a problem. (Note that each loudspeaker is named in full and is therefore easy to identify).
Once you have made the correct assignments to the loudspeakers, you are unlikely to run into any problems. For example, if you assign the signal in the panner of a 9.1.6 bus to a particular loudspeaker, it will end up in the right place in the Atmos renderer and will also be written to the ADM master file.

This Microsoft configuration, which contradicts Dolby Atmos for Dolby Atmos rendering (go figure…) is disturbing. But if we worked in version 12 to adapt the whole system (here I reversed my cables on my Apollo X16), it’s good to stay that way. However, I didn’t see any explanation from SB on this decision. But if this had changed in N13 (where I’m not and probably won’t go), it would have been very difficult for surround users. Stability is a good thing.

Still, it would be nice if Steinberg standardised everything.
If we hadn’t clearly named our input and output busses, I would probably always overlook the fact that the 9.1.6 layout for the input differs in order from that for the 9.1.6 renderer output.

Yes, this is true for 9.1.6. Less so for 7.1.4. But the damage is done…