Transpora seems to be only offering cash/card fares for single, day (£4.70), week (£21) and month. Are you expecting children to have cash or electronic equivalent and does the timetable allow extra boarding time for that?. Does the driver have change for kids with £20 notes for a £4.70 fare, because mum has run out of change. There is no verification that the teenager is a sixth former at the school and not just a member of the public getting a cheap ride. How do you control numbers - children cannot be left behind, when there isn't another bus coming.
There is also the issue that school buses have to run - no excuses - you need backup vehicles and staff on hand. For morebus that's easy, if unkind to the other customers - For Transpora?
You say it as if Transpora is a brand new operator. They may be new to the area but they are headed up by people who have ran a few other bus companies before. Rhys has a history in a number of bus operators and Phillip Higgs of course runs stuff in Blackpool, including Lancashire school buses. I think that they will have covered some of these basis.
As for fares, I'd hope that Transpora do put these fares onto the MyTrip app. They already have the mobile ticketing for Bristol and Blackpool services so I see no reason why that couldn't be expanded. I'd also remind you that this is how a good number of commercial school services run up and down the country, cash or card payments. Mobile tickets for schools have only come about fully in the past year or so.
As for your other points, those issues are not exclusive to Transpora and Morebus, Yellow Coaches and Yellow Buses would have all had the exact same issue. Clearly the demand has been worked out over the past however many years of operation for these routes.
I think Transpora will need more than a few school routes to get started with.
Schools are an excellent place to start. Constant, almost guaranteed revenue. It means when you start normal service, you have guaranteed revenue either side so you aren't solely reliant on the service covering all costs (including depreciation), you can push more of the maintenance and depreciation costs onto the school run and the normal service costs then become simply drivers wage and fuel for those miles. It's how a number of companies run. Schools first, normal service second.
I really hope that Transpora do expand. I think it would be much better for them to have more targeted local expansion rather than a bit here, bit there but expanding bus companies is a good thing surely? More competition and hopefully give local areas a better bus network for passengers.