The insertion point is a result of the ASOBO coding.
Until the Custom FlybyWire creates their own autopilot, or is able to come up with a good temporary fix, it will be a limitation.
You can try putting your HDG on Selected mode (click the bottom of the knob), then steering the plane with the Hdg Knob, trying to follow the course until you can intercept the ILS.
You can also use “DIR” on the MCDU keypad which the FMS will then use to go to whatever waypoint in your flightplan you select.
The flaps are a result of the result of the way the A320 flaps are interpreted in the sim, which gives too much lift when Flaps1 is selected.
It is something you will see be ironed out by the mod crew, as they want the mod to be as realistic as possible!
In the meantime, be as slow as you can when the flaps are first deployed, so you have less lift, and just allow the autopilot to return the aircraft to where it should be, when it starts to happen.
Stay up to date with the mod.
Download the current version before each session you plan to use it in.
Fixes and improvements are made on a daily basis.