Hmm, that clarifies things somewhat. It's my misunderstanding of the apply (square) button, in that case. If I grok this correctly, to apply the PM tool in a global context and have dimensions equal to the input data, I need to plug in the dimensions manually. I don't know how I missed this behaviour in previous versions of PI...
Finally, to answer your question regarding which of the input images you should take the dimensions from; it would make sense to me to take the maximum X and Y dimensions of the set of inputs, even if these figures come from two separate images. It'd be nice if there was a "dimensions from input" option on the dialogue to accommodate this, I suppose. I can make an appropriate post for that elsewhere.
Thank you for clearing up my misunderstanding, both pfile and Gerald. I had the wrong end of the stick entirely.