Merseyrail being ran as a national TOC
Merseyrail isn't a national TOC. It is a concessionaire and that concession is awarded by Merseytravel not the Department for Transport. It exists in the same hybrid world as TfL's Overground and Elizabeth Line concessions.
I tried (and failed) to get a metro card before rail tap and go started, only to be told it wasn't their scheme and they were only as involved as Merseytravel forced them to be.
Sounds like a lazy ticket office clerk to me. I got my Metrocard at James Street (Water Street ticket office) the first time I got a Saveaway, no problems at all.
Though as London shows, you can have integrated fares without needing to run the trains or buses in house.
London's fares are not integrated. London's fare structure is extraordinarily complex.
People simply don't notice or appreciate the complexity of the fare structure because they just tap their card and the computer does all the calculations for them afterwards.
As
@Bletchleyite says, the only integration in London's fare structure comes with the daily/weekly caps and the Travelcard. For single journeys, and even for multiple journeys under the daily cap, the amount you pay can vary wildly depending on what mode of transport you're using and, for trains, who operates the train in question.
The fares structure in Merseyside is exactly the same, with the Saveaway (off-peak day ticket) and the Trio (season ticket). The only other complexity comes with Merseyrail offering an off-peak day ticket only valid on Merseyrail and- disgracefully, in my opinion- setting the price for that at only a few pence less than the Saveaway.
The only real omission is that there isn't a version of the Saveaway which is valid in the morning peak. I'd hope that changes.