And yet, it seems to me that the paint plays a big role if we talk about water resistance. Yet, it is the last layer that comes into contact with moisture.
I am assuming that you mean "first and, hopefully, last layer that comes into contact with moisture"
Design and good counter flashing are probably more important for shedding water. Assuming that the steel is not galvanized, paints biggest role is in corrosion resistance/prevention. Appearance, reflection, and waterproofing are probably considered secondary uses. People were rain proofing structures long before caulk, paint, elastomeric coatings and other easy solutions came along and became detriments to good design and roofing practice. The secret is to really think out all of the possible ways that the water can flow and help it flow off and away..... unless you are building a submarine.
On the roof of the bus you will notice that all of the laps face away from the front so that the wind cannot force water under the lap. All surfaces are curved so that the water has as unrestricted of a flow down off the roof as possible. Diverters and tiny gutters direct the flow away from penetrations and windows, etc. as much as possible Everything is shingled (higher pieces overlap lower pieces) as much as possible. Weep holes (let water drain out) are provided somewhere lower down where they think that a leak could occur. This is design and counter flashing. A mistake here should be corrected/fixed, if possible, and only then think about sealing with caulk or coatings. Most common leaks are around skylights, vents, windows and other penetrations. Correct counter flashing first and foremost. What would you do if caulk was not available?
For instance, the numerous rivets in the roof do not leak because they are squeezed/compressed/hammered into the holes so tightly that they form a compression seal and is an example of good design doing a good job of both fastening, sealing, and not requiring maintenance. If, somehow?, they are loosened they will leak. If they are replaced with pop rivets, then you have a problem and they will benefit from sealing. The paints primary purpose is not to seal the rivets or metal from leaking water. The metal is sealing the roof and the paint is preventing the metal from corroding away. If the metal didn't need corrosion protection, the paint may not be "necessary" but may be used for other reasons - cosmetics, color change, solar reflectance, camouflage, electrical isolation/insulation, etc.
The windows that leak are caused by poor counter flashing and seal designs. Correcting the designs is the permanent solution, not smearing on a bunch of caulk.
Improperly applied caulk actually causes a lot of leaks (damming and trapping water, not sticking, hiding defects) yet people will look at it and and think that "there is no way it can leak with all of that caulk". People that don't understand counter flashing often defeat the counter flashing by applying caulk, creating a dam and sealing off a drainage point or weep hole. "Oh, this crack must be leaking, the idiots forgot to caulk it, I'll put some caulk here and stop that. Gee, I'm smart". I think of caulk/coatings as a last resort and hopefully after I have really thought it out. It is hard to clean up the mess if it doesn't work and it makes the leak worse or diverts the leak somewhere that you can't see it. Then what? You think that you succeeded until.....
Silicone, elastomeric or caulk, makes it very difficult to do repairs later because nothing wants to stick to it and it doesn't stick/adhere to other stuff very well either. Silicone will peel off easily if the surface is not prepped properly. I only used specialized silicone products for certain extreme heat applications (gas vent pipe seals) and some compression seals/gaskets, usually automotive
