I think that in both cases the pickups are out of phase with each other although I can’t be really certain. Is there any certain way to find out apart from just hearing them?
Not that I'm aware of, but it's quite easy to tell from the sound. If they're out of phase, the middle position will sound thinner, with a
lot less bass, than the bridge or neck positions.
But apart the middle switch position which both pickups work together, I’m under the impression that in both guitars, bridge pickups sound better when they are wired on their own. Is it possible to be affected by an out of phase neck pickup even when only bridge position is selected or is it a placebo effect on my mind?
If the pickups are out of phase, you can only hear the effect when both are on - it won't affect the sound of the individual pickups.
However, when you say the "bridge pickups sound better when they are wired on their own", do you mean at some point you had the guitars wired with just bridge pickups, and no neck pickups at all? That could have a
slight effect on the sound, because there's no magnetic pull on the strings from the neck pickup. It's a very small difference though, if it's there at all!