[RPG] When casting a cube spell on a hex grid do you pick a honeycomb for origin or an intersection for origin

No, you can't

You have answered your own question. I understand what you say by RAI could possibly support a "YES", but the RAW clearly does not. You choose how you want the hex to work when you cast it.

Also, Choose one ability when you cast the spell.

The bonus action to move it to a new creature simply moves the hex and doesn't allow or state that you can alter the terms of your Hex.

Scenario 1: The mount is charmed.

If the mount is charmed, then it will probably fall. From the section on Flying Movement in the Combat chapter (PHB 191):

If a flying creature is knocked prone, has its speed reduced to 0, or is otherwise deprived of the ability to move, the creature falls, unless it has the ability to hover or it is being held aloft by magic, such as by the fly spell.

Hypnotic Pattern sets affected creatures' movement to 0, so unless the mount can hover or is being held aloft by magic, it will fall.

It's unclear how long falling takes, so depending on your DM, the rider may or may not get a turn before they hit the ground. If they do, they can use their action to shake their mount out of its stupor as described in the spell. If not, their mount will fall and hit the ground.

If the mount can hover, or is held up by magic, then they still won't be able to do anything, but they won't fall, either.

Scenario 2: The rider is charmed.

If the rider is charmed, things get a little ambiguous. I won't post the entire text of the Controlling a Mount section here for copyright reasons, but suffice to say, it doesn't actually mention under what circumstances a rider can or can't control their mount.

If your DM decides that the rider can control their mount while incapacitated (seems unlikely, but you never know), then the rider will still lose their own turn but can (somehow) direct their mount on its turn.

If your DM decides that the rider can't control their mount while incapacitated, then the mount will act independently as described in the Controlling a Mount section. In this case, the rider will either be sitting there while the mount does whatever it wants, or possibly be thrown off. This is all pretty much up to your DM to decide.

Scenario 3: Both rider and mount are charmed.

As in scenario 1, if the mount can hover or is held up by magic, it won't fall, so rider and mount will stay exactly where they are. But if not, there's nothing either of them can do except fall helplessly to the ground.