it seems to me that the PICKIT_ 3 is loading the BOOTloader when the device is changed from PIC18 to PIC12F675...
How to inhibit it ?
You can't. Different device families needs different things from the PICKit3 and it doesn't have enough memory on board to remember it all. So when you switch families (or switch software from which you "run" the PICKit3) it needs to have a different fimrware image loaded.

There's an issue with using the internal oscillator AND GP3 as IO at the same time. The issue is that as soon as power is applied the internal oscillator starts and sets the IO pins up which now prevents the PK3 from "accessing" it in order to enter programming mode. IF you're supplying power to the device externally then try disconnecting that and power the device directly from the PICKit3, if you're running the standalone application for the PICKit3 look for the Vpp before Vdd setting and enable that (if there is one, I don't remember).

If you spend 5 minutes with Google you'll find threads on several forums (including this one) which discusses the issue. For example, here's one