So, i've just had a brief look at the technical and sporting regulations of the F3 Europe championchip. You're not allowed to swap engines, use your own fuel (or any additives) and a ton of other restrictions apply. You may however rebuild an engine between several events, as long as you don't swap engine block, head or cam cover. That'd count as a new engine. I'm not sure one could exploit this to get a fresher engine than others.
So, i must admit that i'm a bit sceptical that anyone can cheat for a better car/engine. The only thing i can imagine is that the different engines (F3 europe has different engine manufacturers) have slight differences in either power or torque. That'd result in some engines being slighty "better" than others.
My conclusion is that Prema must have found something setup wise or that Ticktum is just being salty because he basically has almost lost the champoinchip at the last two venues.