I don’t see how either of those affects punctuality that much.

Small just means that more of your trains will be arriving from a different country, so you have to compensate for their shitty scheduling. Like I once took the train from Bulgaria to Turkey, and was told it’s usually late, because the same train had to arrive from Serbia first, and it would habitually show up two hours late. If you’re a bigger country, or not connected to anyone else by rail, you would have more of your trains fully in your own control. Switzerland is basically a rail hub for Europe, so it should be harder for them, not easier.

Flat seems mostly irrelevant, since rail has to lie mostly flat anyway. This would be an impediment to rail construction, not punctuality. Although rail construction could of course be an impediment to punctuality in that lack of tracks makes scheduling harder. Double rail is a lot easier to schedule on than sharing one set of rails for both directions, and those extra tracks are more work to add when you have to make a lot of holes in the mountains.