There seems to be some confusion here. I think by "no you cannot" the first response meant "you cannot verify that it's impossible". Beam PD assigned to a fire control can fire on another ship just fine. CIWS can't fire on ships, but they're not assigned to a fire control.

None of the built in PD modes will target another ship, but if you have the fire control the beam PD is assigned to target another ship directly instead of using a fire mode, it should work.

If you are within range (accounting for enemy jammer and stealth), you have active sensors on and you have BFCs with weapons assigned you can target enemy ships.

Any weapon can be used as PD (with more or much less effectiveness depending on the weapon, turret speed, BFC speed and range and the reload rate), you just need to assign a PD behaviour to a BFC (right part of the combat tab of the naval organization window when you have a ship selected).

Since PD weapons are just normal weapons with assigned PD behaviours you can just assign an enemy target to a PD BFC and order the BFC to open fire as normal.

No you cannot.
Beam fire controls can target any ship within their range. If you cannot target the ship shooting you, check that you have active sensors which are on , and that the Alien race are set to hostile.

I agree with the above... a layered defence is absolutely the most effective option in the long run. Early on you might only rely on regular PD and possibly decoys depending the techs you have researched. It also is quite possible to rely entirely on PD such as say railguns if that is the technology you have chosen to focus on for some roleplay reason.

Focusing on AMM only is of course possible but certainly far from optimal, you wold at least want to have good shields as a secondary way to absorb leaking missiles.

I rarely also build strictly focused ships on one type of weapon system. The reason is that it is much more efficient from a yard perspective to have multiple weapon system in less designs that you can build in the same yard with only slight differences on weight of weapons systems for the current needs you have. It also makes upgrade cheaper and less costly in time due to how research is progressing. It is quite rare for me to have a ship that only have PD guns on it as a fleet are going to have a layered system anyway. It is also more vulnerable to put all eggs in one basket as that means you can more easily knock the more important system out which will lead to a domino effect. This is mostly visible when you command multiple sides of a conflict at the same time.

You don't need to be afraid to put allot of AMM launchers on one fire control, at least not if the rearming of the launcher is more than 5 seconds. They will continue shooting every five seconds of the missiles if the salvos are smaller the the number of AMM missiles you want to fire.

I actually rarely fire more than one AMM per incoming missile as I don't want to waste AMM but use a layered defence of PD, CWIS and shields. I don't like wasting AMM if I don't have to.

For beam PD you theoretically only need one FC for all PD weapons although you usually want at least a backup FC. One fire-control can target all incoming salvos. One turret can only target a single salvo though.