The C64 Core does not currently support alternative kernal selection via the Kernal Selection menu. It would be a nice feature to have in the next release of the C64 Core.
Similar to the operation of the MEGA65, perhaps there should be a ROMS folder in the C64 folder containing the custom kernal ROM files which the C64 Core could look for.
Include support for reading custom charset ROM files and custom BASIC ROM files and then folks will truly be able to customize their virtual C64 to their liking!