Hello,
I am afraid that all what you said is totally valid.
The lack of support of "hydrid" documents by XLIM is something that we warn our customers in advance, so we promote the use of InDesign Server instead.
If I look at the internal structure of a XLIM file, that was exported from an hybrid InDesign document (in size and/or orientation), it only features one single "fo:simple-page-master" element, with the size and orientation of the first page, not taking the rest into account.
If I play, and manually add an extra "fo:simple-page-master" element with the size and orientation of my second page, then assign this master to the 2nd page in the XLIM document, composing from uProduce does not take these hazardous changes into account, again - I obviously do not recommend trying such changes on a production machine, as it may be way out of what the XMPie Support Teams would like to see in the field.
Also, as you were referring to uStore, I assume that you also may want to use such hybrid XLIM documents in uEdit NG? As it relies on XLIM - with some limitations - no need to say that it will not work neither.
I agree that the XLIM Preflight in uCreate should raise some warnings or errors, upon detecting such attempts.
Or, investigating if some Rotate / Resize steps of FreeFlow Core Advanced Prepress could help?