On Linux, you run windows programs through wine, which is an additional layer that can theoretically slow down the program.
Also, windows supports certain constructs like io completion ports or WaitForMultipleObjects that historically haven't been emulated efficiently on Linux since it lacked comparable primitives, although those specific ones have been greatly improved in recent years with io_uring and FUTEX_WAIT_MULTIPLE.
There have been similar issues with direct3D since wine used to have to emulate it in OpenGL, but with vkd3d, wine has more opportunities to efficiently implement the d3d apis.
Basically wine being slower was the norm until quite recently.
There are complicated parts of accounting, but basic expense tracking is simple and businesses would do it even if it didn't affect their tax treatment.
If businesses couldn't write off expenses, it would be nearly equivalent to treating the corporate income tax as a universal sales tax. This would be incredibly damaging to small businesses and benefit behemoth vertically integrated companies, which is probably the exact opposite of what you want.
If you get rid of expenses, you need to get rid of corporate income tax and either replace it with VAT or combine it with increases to personal income tax like taxing capital gains as ordinary income.