Boeing's plane was so heavy they had to remove panels before it could
even hover. Neither aircraft could stay in the air more than half an
hour without refueling (Boeing's Navy style in-flight refueling system
was not operational and so they had to land every half an hour to
refuel). Neither plane had any armaments or weapons during all of
this.

Keep in mind that these were PROTOTYPES, hense the experimental
X- designation. Once a winner is selected, they then go to full
scale development, which are Y- designations. That could take a
number of years, and the final plane might look very different
from the prototypes. Look at how much changed between the YF-22
and the F/A-22 that finally emerged. Dittos for weapons, that
comes in the Y- program.

Adding a bit here... they X- prototypes were not intended to be
representative of the final production versions. Aerodynamically, maybe
(and not even that in the case of the Boeing design), but their fuel
capacities were far below what an operational aircraft would carry. Also,
the weapons are pretty much standardized (most everything that's in the
inventory now), and testing them with a pre-development aircraft is pretty
much useless. The big issue will not be whether the aircraft can talk to or
emply the weapons so much as separation and clearance and such... and that
wouldn't be too much of a problem. Avionics interface testing can be flown
on other testbeds or on the preproduction aircraft.

As stated above, the two ATF prototype aircraft were only somewhat similar
to production aircraft. Neither of them carried radar or an operational
amount of fuel, and neither were equipped to use weapons (though a dummy
round was test-launched from the YF-22).