All in all it seems ok, since booting from the MMC and from the flash will end up in having different themes, different brightness/volume settings, etc.
*But* I cannot understand this: I partitioned my 1gb MMC into about 800 MB + 196 MB partitions to have some 64 MB more than the usual (the calculations were: 128 MB flash with normally about 64 MB available on the device so 196 will provide the 64 for the system plus 128 MB for applications).