I basically followed the guide and skipped the EmuMMC installation portion.
There should be an option there to specifically get CFW on Sysnand.
And I don't see why you're asking if you can still go online on CFW on Sysnand. I literally said that's what I'm doing. I use the e-shop, have the DLC, do online wild area battles and everything. I can't give you any more confirmation than that.
In reality, all I think you need to do is transfer you saves over to Sysnand, back up your Emunand partition, then fully format your SD card (to wipe the emunand partition). Alternatively, if you're using Hekate bootloader, it should give you an option to boot straight into Sysnand with CFW.
Then, go ahead and update your games, download the DLC, before going online.
In any case, all this will be at your own risk.