Apparently, the 20mm cannons on the Cheyenne do the same damage as the pulse rifle the marines in it carry in their hands?
If this sort of conflict only happens once in a blue moon,
Personally, I'd ride right past this and just focus on "story and effects" rather than simulation rules.
And, I'd probably scale the Cheyenne cannon to be at least a smartgun / robot sentry worth of damage rather than pulse rifle.
If vehicle weapons are on the same scale as characters, does that mean starships can't target vehicles, thus a Cheyenne can harass a Conestoga and 'Stoga can't shoot back?
Two different cases here - in space and in atmosphere.
In space, the frigate should have the advantage.
In atmosphere (such as when we see the Patna landing in ALIEN3) the Cheyenne should have the advantage.
And even if there's no "rule as written" on when/where vehicle to vehicle combat works - common sense should still apply.
In both regimes - both vehicles can target and shoot each other - there's no magical force or law of nature that prevents it.
But, you can handwave lots by just having the sides miss or not, etc.
A Cheyenne does damage - but very little due to difference in scale.
One system that I very much like for this is that when scales or so different - damage to the larger scale object is done to "subsystems" rather than overall.
A Cheyenne shoots up one landing bay ... that system is down... the rest of the ship carries on.
Are even the Cheyenne's missiles ineffective against a starship's armor?
Personally, I'd rule that starships are aerospace vehicles and very, very vulnerable to damage.
"Armor" on an aerospace vehicle isn't like a 20th century wet navy battleship.
It's more like "hardening" specific areas or subsystems.
Overall the entire vehicle is still extremely vulnerable to interference with given areas of the ship.
Shoot it - you hit a wiring conduit - is that armored against missiles?
As Rocket Cat says: in space, every gram counts - you can't just carry meters thick slabs of armor and expect the ship to still be able to move...
Can an Alien claw its way through an APC's armored hull to get at the tasty marines inside?
Yes - given the scenes in ALIENS where they ripped through barricades, and even welded shut doors.
They are smart enough to find weaknesses and exploit them, including just ripping the door open.
Plus, players should never feel "safe" - an APC isn't a panic room.
Its a vehicle armored against flak and shrapnel and such - but its still but soft spots... somewhere... like those windows or that big sliding door...
We live, as we dream -- alone. ~ Joseph Conrad