Check out the parts diagrams yourself. Available here under the download sections for both models.
https://www.tohatsu.de/en/outboards/four-stroke
Interestingly, the 3 fuel injectors are the same but the intake manifolds are different, but a lot of parts are the same, I suspect with model variations codes on identical parts.
The MF60A is new engine and comes with a 7-year Tohatsu warranty so spend the additional €1,500, knowing that if you come to sell it - it has history and a paperwork trail which future buyers will pay a premium for.
Incidentally, the ECU assemblies are different. I can't even find a price for the ECU on the MFS60A given it's a 2020 model. The MFS40A and MFS50A ones are in the region of $950.
I don't see any savings to be made.