Not really, you will just be confusing yourself more.

99% of card effects don't apply in private knowledge, except those cards that specifically said so.

If a card would say "while this card is in the deck: yada yada yada" then it would activate from deck, otherwise not.

Fusion substitute has what's considered a condition. Not everything in a Yu-Gi-Oh card text are effects, sometimes those are conditions or more frequently, activation requirements a.k.a. "paying cost", those also not an effect. Different rules applies to them, i.e., they can't be negated as no card in the game negates a card condition, just the effects.

To differentiate this, checking yugipedia or the sort is your best bet. Eventually you kinda get the gist of it due to wording, even then, i still check yugipedia if some niche scenarios come up, just to be sure.

In short: fusion substitute has a condition and swamp has an effect.