After you load the bootloader into the chip (using the ISP port and and an external programmer) it will work like any other Arduino.
...I think you're "nuts" to build your own unless you want to make your own special version with extra circuitry, or without circuitry that you don't need. There's a LOT that can go wrong!
That is only a small part of the UNO WiFi Rev2. The main processor is the atmega4809, the atmega32u4 functions as a USB to Serial interface, and a UPDI programmer for the atmega4809.
You picked a particularly complex Arduino board for this project.
Its a really ambitious undertaking for your first board (if it is your first).
To your question, if you replicate it then the Arduino IDE will not know the difference between yours and a real Arduino. So yes you can compile and upload to your hearts content.
However there are physical rules that are not on the schematic. For instance the location of the crystal and its caps is critical and could cause an otherwise properly connected board to not work. Grounding is also critical on a board design. And don't be too surprised if your 1st board doesn't work. The process to go from a paper design to a finished working PCB is much more difficult that it seems on the surface.