You don't need to remove the bootloader in order to upload Arduino-less code.
The bootloader is just a piece of software that is loaded in the AVR that allows
a tool (avrdude in this case) to upload code to the AVR. The bootloader itself
is totally independent of anything Arduino.
As shipped the AVR fuses are set to create two sections in the FLASH. Bootloader and application.
The "Arduino" bootloader is small piece of code in the AVR that uses the serial port to update the flash
with the user application (code/program/sketch).
The bootloader runs at reset/powerup if there is no attempt to upload anything, the bootloader
will start the application code.
The application code can be written using any toolset you prefer. The Arduino tools are just one option.
avrdude is a tool that is used upload code into the flash.
avrdude can be used with an ISP programmer to upload code to the flash
avrdude can also use other mechanisms like a serial port that talks to a serial based programmer or to a bootloader.
The Arduino IDE uses avrdude to talk over a serial port to a pre-installed bootloader in the AVR chip.
The newer IDE can also use an ISP progammer to upload code. When an ISP programmer is used,
a bootloader is not used so the flash space used by the bootloader code frees up and can be used
by the application code.
If you don't want to use a bootloader, you will need some sort of ISP programmer.
Like Pico, I recommend getting a USBasp programmer off ebay.
I like the USBasp kk multicopter programmers (about $5-$10 USD) because they come with a 6 pin ISP
cable instead of 10 pin so no adapter is needed.