Mono’s and stereos together inside a folder would cause problem as you have already seen.
With only stereo files, the file will be played back on 2 channels. So the numbering has to be done carefully by the user, which is error prone.
We have not extensively tested all the scenarios with stereo files in multitrack and thus cannot vouch for it.
If this is a useful feature, maybe we can have a look at it for the next firmware update.