alasdair1
Couple of suggestions.
First, these flights to which you refer, both TCX and TOM are essentially vehicles to get ITX passengers to accommodation that the respective (vertically integrated) tour operators have contracted. If TOM has a higher proportion of seats sold / allocated to ITX passengers, then they will have fewer "flight only" seats available, which would therefore command a higher price on the dates you book / make a test booking. It may be that TCX commits more seats to "flight only" passengers, or wants to attract more flight only passengers and therefore targets that market segment more aggresively.
Second, two words "yield management". The company pitches fares to reflect demand, cost of seats already sold, number of seats remaining - and probably a ship load of other factors.