No, you don't need to do that at all.

Lesson One: Anything with "wiki" in its title can and probably will be wrong. Don't believe anything you read on the internet. Not even what I'm saying! : )

The Wiki on reflashing the N900 is seriously in need of simplification. It is ambiguous at best, but really, it needs to be deleted and rewritten.

Moving on.

It very literally does not matter what order you flash the two files in, so long as you get the flasher syntax correct for each one.

Ideally you would first flash either the emmc or the rootfs without the reboot switch, followed by the other with the reboot switch. Technically it doesn't much matter if you do reboot for both though, just that it'll take you a couple extra power cycles to get the job done.

The Wiki, once you strip out all the guff, tells you to do the rootfs first, followed by the emmc - so you are wrong.

rootfs: RX-51_2009SE_20.2010.36-2_PR_COMBINED_MR0_ARM.bin
eMMC: RX-51_2009SE_10.2010.13-2.VANILLA_PR_EMMC_MR0_ARM.bin