This is quite hard to answer. but let me try this, Well even though it's exact use more memory in when booting from flash, but the rootfs stored in the flash is in jffs2 and in order for the data to be usable, it got to be uncompressed first, right, so where is that uncompressed data stored?
the main reason why the system is slow when booted from flash because, all the application(not data stored on SD/MMC) are pretty much in compressed format. The CPU is already underpower at 300MHz already, and now it have to do compression/decompression on the fly, it's another step for the CPU to handle.