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Fan -> Fan Controller OR Fan -> Mother Board?

Level 7
I have the Maximus VI Extreme in an NXZT Phantom case. Four of the six fans came pre-installed
and connect to a pre-installed fan control module which connects directly to the power supply.
The additional two are part of the liquid cooler.

The pre-installed fans do not interface to the mother board. Fan speed is controlled by individual
slide switches. Without the mother board connection they are not being monitored.

My Questions:

Is it better to run these directly from the power supply vs: Fan headers on the mother board?
Does mother board power to the fans introduce more electrical noise into the mother board?

Since the pre-installed fans all have male gender connectors and so does the mother board. Can I
simply cut off the male pins and replace them with females so that they plug onto the mother board?

Level 7
I think it would be a matter of personal preference.

I myself don't like having to use switches to control fan speed, I prefer to set up a curve in bios and/or software. But since I also use linux few controllers has software that work in Linux (unless you find some third party) so I simply use a pwm splitter cable from the fan header on the motherboard and has separate power directly from psu.

About replacing the pins you would probably have to Google those specific fans first to see how the wiring is done. Guessing they are 3 pin (most fans that come with a case is usually 3 pin). Then it would be like this:

To replace the pins you would also need decent crimping tools, and molex has good pins with a bit longer "wings" or what to call it to hold the wire better.

Edit: ignore the written colors on that image, the seem to be a bit off and don't even match the numbers on the image