At weekends, if I want a travelcard from my local station (Horley), the cheapest ticket I can get is an off-peak travelcard. However, if you go from Three Bridges*, there is the option of a cheaper super off-peak travelcard (even though you are further away).
You can use the Three Bridges ticket starting at Horley - "break of journey" is allowed at intermediate stations.
So two questions,
1 - is there a difference (additional restrictions) between a ‘super off-peak’ and a ‘off-peak’? Both are ‘Thameslink Only’.
On a weekend or Bank Holidays, both of these fares are valid all day, so you can just buy the cheaper one.
However this isn't the case for all Super Off-Peak tickets; some, primarily those set by West Midlands Trains (London Northwestern) and SWR, still have restrictions on Saturdays.
2 - why is the super off-peak option not available from all stations?
It's down to the complex history of the fare structure on the Brighton Main Line. Thameslink created cheaper fares for journeys such as Gatwick and Three Bridges to London, back when they were a separate franchise and operator competing with Southern. They didn't serve intermediate stations such as Horley, so they didn't create "Thameslink only" fares for travel from those stations to London.
The situation is now reversed, with many of those stations now only (or primarily) being served by Thameslink, however the "Thameslink only" fares were kept after the creation of the Govia Thameslink Railway franchise in 2015, which merged the previously separate Southern, Gatwick Express, Thameslink and Great Northern operations.
The "Thameslink only" fares thereby became valid on all GTR services, as there is no legal mechanism in the National Rail Conditions of Travel to restrict travel to one particular brand, only to a specific train company (and all of the above brands are operated as one legal entity, Govia Thameslink Railway Limited).
There have been various suggestions/threats to withdraw these cheaper fares over the years, though it has not materialised so far. However, I do I expect that it will happen when contactless PAYG is extended towards Brighton.
A "simplified" Project Oval fare structure (i.e. one that's much more expensive for most Off-Peak journeys) has already been rolled out across other routes where PAYG has been expanded, so we can look forward to more of the same

.
Sadly this is what the government claims people want. What people actually want is for travel to be both affordable and simple. But the government is using this as an excuse to make it
appear simple on the surface ("you can just tap in and out"), whilst actually being more complicated under the hood (Off-Peak paper tickets will apply at different times to PAYG Off-Peak fares, for example).and quietly increasing fares (and thus rail industry revenue).
*Super Off-Peak tickets were also recently available from Gatwick, however they have disappeared there now.
We'd need to know exactly which Super Off-Peak fare you're referring to there (e.g. what price?) because there are a lot of different ones. Super Off-Peak fares are absolutely still available from Gatwick.