Reluctantly

You know I'm afk, and you still kill me.
Also, I have no idea how you got in.
Classy act.

Yeh the glitches sadly are part of Minecraft's physics, luckily we keep most of them secret

Do yourself a favor and make all your walls two blocks thick. Also, put redstone dust on each side of your door to keep out the people who will try to pearl.
Or just build in the sky.

1. Cloak:
» can be bought for 3000 greencoins and (currently) is permanent when bought
» gets enabled by

ticking /cloak in the chatbar

» gets disabled by

ticking /uncloak in the chatbar
Hitting another player (60 seconds delay before you can cloak again)
Getting hit by another player (60 seconds delay)
Getting hit by a mob (60 seconds delay)

» doesn't gets disabled by

logging in/out
dieing by falling/drowning etc.
Hitting a mob yourself (as long mob doesn't hit you)

2,3,5
There are many glitches, building a really safe base won't be easy
Mob spawners
Ofcourse this is allowed otherwise experience could better be disabled

Yes. But you don't really need to be cloaked all the time, do you?
Not all people know about dynmap anyway.

Sorry if these are FAQs, but...
1. Can people hide their presence on the online live map? If so, how does one go about doing this?
2. Is there a 'boat glitch' that allows players to go through blocks, even in another faction's claimed land?
3. Can players hit doors repeatedly and get through using an ender pearl?
4. Mob-spawner farming is allowed, correct? Idk why it would not but I suppose it could lag a server.
Thanks!
5: Is there ANY glitch at all that allows you to go through blocks in another faction's claimed land? I have been having a pest get in somehow and I am fairly sure I have checked time and time again how he gets in. A glass hallway type thing is 1 block below the surface of the water... This is how I imagine he gets inside the base, but how does he do it? Thank you, again!

you can by buying the cloak perk from the greencoins shop.
Edit
yeah there are numerous boat and enderpearl glitches and mob farms are allowed but yeah it can cause some lag.