EMP Grenades/Bombs
So I just learned from Are Gatekeepers vulnerable to EMP Bombs? that Gatekeepers can actually be heavily damaged from EMP grenades/bombs, and can even have a chance to be stunned by them for 2 turns!
I tested and confirmed this myself. In the following screenshot, I used an EMP Bomb on an undamaged Gatekeeper, and it took something like 12 damage, and was also stunned:
Which is weird, because you can't hack a Gatekeeper, so who knew it had robotic components that could be damaged by an EMP?
Flashbangs
I've heard that Flashbangs (or being disoriented) can lower a target's Will stat, which would make it more vulnerable to mind control. I decided to test this out too.
The following is the Will stat of an undamaged Gatekeeper versus a fully upgraded (i.e. has all abilities and fully upgraded Alien Psi Amplifier) Psi Operative using Dominate:
The target's Will is 110%, which reduces my chance to Dominate to 80%. After hitting the Gatekeeper with an EMP Bomb, followed by a Flashbang (so that it's also Disoriented), I checked the chances again, and the Gatekeeper's Will was still 110%.
I've also heard that Flashbangs (and being disoriented) can disable some of the Gatekeeper's abilities, but I haven't tested this out yet, and I'm not sure which abilities exactly would be disabled.
No, the idea of the Commander is that you, the player, are the Commander. The gender of the Commander is your own (or whatever you want it to be). As you've noticed, the game carefully dances around assigning a gender by only strictly referring to you as "the Commander" and refraining from using gender-specific pronouns.
This is backed up by the wiki page on the Commander:
You play as The Commander, who is the main brains behind all of XCOM as he/she manages the XCOM project. He/she decides everything that happens from; what research project to start next, to commanding the troops on where to move on the battlefield. The commander's true form is completely unknown implying that you (the player) are the commander.
Further down the page, it also has gender listed as being unknown:
Gender: Unknown (either male or female)
This is actually a trope featured on the game's TVTropes page for the characters in multiple places:
Ambiguous Gender: Their gender is never referred to in game, allowing any player to identify with them.
Featureless Protagonist: The Commander gets an in-game model... as a bulky self-contained suit that obscures any identifiable features, including gender. All the better for the "self insert" Non-Entity General role taken up for the rest of the game. The Commander's Avatar looks like any other.
Best Answer
Gatekeepers are the highest armor enemies in the game. They are also pretty much at the end of the alien power tree. So, it shouldn't get any harder quality wise, only in terms of quantity.
The strength of enemies is a mix of time and your strongest possible squad. If you have a bad early game and don't manage to get higher level soldiers, the difficulty curve will rise slower than when your main squad just aces every mission and you have a troop full of colonels by July.
Difficulty also plays an important role. On Legend difficulty all progression is slowed down a lot.
In general aliens reach top tier troops between September 2035 and February 2036 on lower than Legend, on Legend it's more like December 2035 to May 2036.