Yeah that was a rough addition to smooth out in geosphere. The confusion was because the PQ data is as-of PQ generation date, whereas if using the API, the caches contained in the PQ are still as of generation but the data itself downloaded from the API is current. That is to say, if you generated a PQ 3 days ago, and new caches are published that weren't there 3 days ago, they won't show in the PQ if you download it (via any method) today - even though you get logs on those older caches that were posted today.
It was GS's combining of temporal PQs with current API functions that makes it confusing That was one reason I like the ZIP download - no confusing data, as long as you realize that all the data is only as of the generation date. If you want current data in a PQ, you need to generate the PQ right now, then download it (by zip or api). No way around that in any app. At least until the API allows generating the PQ and downloading it together (or maybe just uses the PQ search parameters to do a current API search and download).
But anyway.
I haven't used the ZIP pq download for a while. That import ability was good mainly for downloading the My Finds PQ, which as I recall isn't provided by the API - have to generate the PQ then manually download the ZIP from the web and import into the app.