"However, the problem is, that random note is also being played by EZkeys inside FL Studio, ruined the song."
It's just a routing issue you have EZkeys set to take incoming midi, I'm sure in that video he went through that if not look at some other videos.
I don't use FL I use Reaper and it's just easy to set what midi comes to the VST from another track or hardware, FL would be the same.

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