Some railways give the Trainline a commission, other don't. That explains why there is sometimes a booking fee. But I do not have the impression they are overcharging you. Trainline (the European one, not the UK one) was started by a group of French train enthousiasts that were getting fed up with how bad the SNCF website was. It was originally called "Capitaine Train".
The current incarnation of RailEurope started as Loco2, a UK shop that basically did the same thing as Capitaine Train. This explains why Seat61 likes them. They asre usually quite good.
However oddly they appear to be a lot more expensive than SNCF themselves for local trains in France.
My golden rule is: Book train tickets with the national railway of the country where the trip starts, or the one where it ends.
When reservation costs are listed separately on a ticket that means that the reservations are not compulsory. I would reserve long distance trains in Germany, but in Switzerland this is not necessary. Nobody does that here.
Paris - Bayeux you buy at sncf-connect.com. If you buy those a few days in advance you get a nice discount. A full flex ticket bought at the station is however 43,- so that is where that 100USD return RailEurope offered you cam from.
Paris - Montreux buy at www.sbb.ch, or www.trainline.com as the SNCF cannot sell you tickets for local travel in Switzerland.