A filter stops or blocks and holds particles larger than size x. Smaller ones flow through. If these particles are still smaller than the smallest orifice in the carb, they flow through it and the engine and out the exhaust.
Who cares? Well there may be issues when the fuel is NOT flowing.
Anatomy of a rust particle.
You've seen severe rust scale. It's clumpy with jagged edges. Its heavier than gasoline, too, and settles into low points with gravity. Well, the small bits of rust are jagged, too. The ones that get past the filter and into the carburetor fuel bowls, settle to the bottom and interlink with others, forming larger ones (even flakes) while the bike sits without fuel flowing through the carbs. These larger ones can block the small orifices, usually the slow jets, and can also keep the float valves from closing completely, causing them to overflow.
Lastly, rust particles of any size are abrasive and can cause wear to occur more rapidly where any part of the contaminated fuel contacts metal. I.E. Carb slides, float valves, cylinder walls, valve faces, petcock seals, etc.
Rust is bad for machines. It will eventually block fuel filter flow and starve the engine for fuel. But, I can't tell from the problem description if rust or filters are the direct cause of your performance issues.
Cheers,
