Playing a mission today, I tried to place a Holy Hand Grenade between two items (a girder and land), and the space between the two places was certainly not wide enough for a Holy Hand Grenade to fit through, yet it did, unfortunately for me (though I completed the mission anyway).

Check out the attached save-file, at around 14:35.

Not sure if this is intended (which I'm assuming it is, because I notice this type of behavior throughout the game all of the time).

That's perfectly normal - the sprite's always much larger than the collision mask.

All projectiles have the same 7x5 pixel collision mask, regardless of the weapon sprite that is used.

That's interesting... thanks for the clarification.