This is a display problem on the Nios® II SBT; the public.mk file is compiled according to the settings in the public.mk file, so it works as configured on the actual device without any problem.
If you want to reflect the grayed-out settings, Clean Project the Application and BSP, and then Build Project the BSP.
This applies to more than just the enale_small_driver setting.
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Category: Nios® II
Tools: Nios® II EDS
Devices: -