the radiator cap is a pressure cap
when the pressure in the cooling system exceeds the pressure rating of the pressure cap, it relieves the pressure into the overvflow bottle.
Conversely, if the overflow has coolant in it, when u turn off a hot engine, the coolant will contract, which causes the pressure cap to allow coolant to be drawn back into the system, thus creating a closed system.
--BUT--
for everything to work, everything except the overflow bottle has to be sealed up good. A crack in the cylinder head causes an air leak of sorts. Combustion pressure leaks out (and causes aeration and overpressurization of the cooling system), AND the cooling system won't "suck" coolant back in as it cools down.
Kubota heads crack pretty easily after an overheat event. So don't overheat them.
On the 900's, they don't have that bleeder. X900's do.
On the older 900, prepare yourself to replace these items if you coolant is or was every rusty-looking:
radiator
water pump
thermostat
head
head gasket
ALL hoses (including the little one from the water pump to the pipe)--and on some RTV's also the trans oil cooler hoses.
and you'll also need to flush the block out, and clean the junk in the passages at the top of the block--they get plugged with scale (rust) and will also contribute to overheating. These are often overlooked by even seasoned techs.
why replace the hoses? Because junk coolant conducts electricity, which causes the hoses to soften and eventually they'll leak. Sounds crazy but it happens. Often. Also contributing is the fact that combustion gases have gotten into the system which also causes the hoses to soften.