There's no need to activate your pass (or any travel days) in advance. In fact, it's better not to do that because you can only cancel activation until 23:59 before validity starts. If anything happens after that, e.g. you wake up ill, then it will be too late and you'll loose travel days.

The rail planner app is not updated very frequently, so your trains may still be missing. You only have to add it before you board it though, and usually the app will have been updated with the correct schedules by then. If not, you can always add a missing train manually.
What trains are missing in the app for which dates and departure times?

A QR code will be available in the app after adding a train to your pass and tapping on "Show ticket". There will be one QR code per travel day. See the instructions here:

https://www.interrail.eu/en/interrail-passes/interrail-mobile-pass/getting-started

To book a reservation however, no active pass and no active travel day are needed. It's also quite useless because you can cancel activation as long as validity hasn't started. This means your ticket office should just have booked your reservation. You can also book it yourself online. For LNER trains, you can use their website or app (with seat selection); for all seat reservations in the UK, you can use GWR, see instructions here:
https://www.seat61.com/interrail-and-eurail-reservations.htm#UK

To book other trains, that page is also very helpful, since the Interrail website is rarely the best place to book. It's more expensive, has worse refund/exchange conditions and has often strange errors.

We have - rightly or wrongly - activated our passes.  

however, having read your reply, i have unselected the Travel Days

the journeys are in the planner but not toggled

the missing trains that we have tickets for are

19th April

17.04 - 18.50  Milano / Firenze

4th May, we've booked the 15.12 - 16.30 Paris / London

Our UK tickets have to be bought locally but the ticket office can’t issue against a reference number; must be a QR. 

Seat61 suggests

- Reservation on all other trains in Britain is either unnecessary (suburban & local trains) or optional (longer-distance trains).  You can just get on any train, find any empty unreserved seat and sit in it, showing your pass when asked.-

which sounds good but our ticket office tells me we risk a fine as it is not accepted without a QR code to scan

The best is to cancel pass activation too and only activate on your start date.

That train is in the app. It does not depart from Milano Centrale but from Milano Rogoredo.

That train is in the app. Maybe you need to check for app updates.

Please don't confuse tickets and reservations. Your pass is your ticket. You don't need to buy any other tickets. Reservations are separate.

Your ticket office is incorrect and doesn't need a QR code to issue a reservation. It's the first time I've heard this about a UK ticket office. If they insist, you can activate a future travel day, show the QR code, and then cancel it again. You only need the QR code on the train and to pass any barriers at the station.

All UK day trains with reservations can also be booked online via GWR, as I wrote above. The rail planner app and the Interrail website don't mentioned GWR; I don't know why but they've never been complete.

This is very comprehensive.  

Having worked out that QR codes are by the day, I came to the same conclusion. 

I’ve activated the travel day for Outbound and Return Day to gain QRs for these, so will tackle ticket office later.

progress report to follow,

The ‘missing’ 15.12 re-appeared when I loaded my partner’s Pass .