Configuration variables cannot be set/overridden by target specific variable values

[Virtual-Java]

I'm trying to implement a makefile inspired by these used in optiboot bootloader.
https://github.com/Optiboot/optiboot/tree/master/optiboot/bootloaders/optiboot

Then I want to create a makeall script, that compiles the hexfiles for all microcontrollers, which will simplify to generate multiple hexfiles for different configurations of my Multihoodloader.
https://github.com/Virtual-Java/HoodLoader2/tree/multihoodloader/avr/bootloaders/HexFiles
Furthermore it may be useful for users of your Hoodloader2 too.

It is not possible to set/override LUFA configuration variables by target specific variable values.
e.g. the following target specific expression in makefile will be ignored. Instead of the target specific value the globally declared value will be taken when calling "make atmega8u2".
abcminiuser/lufa#175

Maybe you can help me to solve this issue.