If the windings are on opposite sides of the core the isolation is good but the coupling is not. If you are trying to move power you want good coupling.
How much isolation do you need?
I have had magnet wire hold to 1kv, it should not be used that way. If you 2KV I know of better wire.
To get max power and min noise I would, start at the CT point and wind bifilar. Example: wind 10, then two more turns on the primary.
Example: wind primary 2T, wind bifilar 10T, pull out the CT, wind bifilar 10T, wind primary 2T. This keeps the AC losses and noise down.
On the other hand I often run supplies at 10x this frequency and fight AC losses.
Go ahead and wind any way you want for the first try. It will work.
I don't know what core you are using and if that will work!