If I buy a super off-peak ticket, can I travel on a off-peak train and pay the difference?

According to https://www.railforums.co.uk/threads/railuk-fares-ticketing-guide-section-4-excesses-upgrades-supplements.70374/#post-1185795 yes you can, and there is no penalty for doing so on-board.

Note that for a return ticket, the price charged for the excess is the full difference between the original return ticket and the return ticket you are excessing to (unlike a change of route excess where you can excess half of the return ticket for half the difference in price). In some cases it may be cheaper to buy a new single ticket than to excess a return.

Contrary to what others have said, there is no administration fee to pay to obtain an excess for a flexible but time-restricted ticket. That would only apply if you held an Advance ticket (i.e. fixed to one or more specific trains) and wished to travel on a different train to that which you had booked.

Indeed, if it were not for the fact that Paddington station has ticket barriers on almost all platforms, then you would perfectly well be entitled to get the excess on-board the train - regardless of previous ticketing opportunities. This right is given by Condition 9.5 of the National Rail Conditions of Travel.

So in your case you should be charged the difference to the £44.10 Off-Peak Single route "via Stroud" if that's the one that is valid at the time you want to travel. So that would be £11.50 assuming you don't hold a relevant Railcard.

In practice I agree that many ticket office staff will claim that this is not possible due to a variety of spurious excuses, such as you having bought the ticket from another retailer, the fact that you bought it online, or the fact that it is a non-paper ticket. Some may even claim that you can't obtain an excess for time restrictions at all! A few of these reasons may be physically true (i.e. the clerk would get in trouble with their manager if they sold the excess contrary to internal company policies) but none are legally valid reasons to refuse to sell you the excess and to refuse to let you travel.

If you do, therefore, wish to travel during a time your Super Off-Peak ticket isn't valid, and you are unable to extract the required excess from a ticket office, I would make sure to have some kind of record of this (e.g. covert audio recording - contrary to popular myth this is not illegal in any way, even if some may find it discourteous). Then pay whatever they claim it is you need to pay, and raise a complaint afterwards seeking to recover the overpaid amount (and escalate this as required).

It's shambolic and unacceptable that there are cases where passengers have to be out of pocket to exercise rights the industry has chosen to give them, but poor training or misinformation is rife across the industry and the only recourse, in some cases, is to ultimately resort to the County Court. Unfortunately.