I just purchased a BDP-S3100 and my experience matches with yours. Somehow I managed to miss this message about the WOL being useless, which is unfortunate. However, I added it as a Series 9 Device, once as an IR and and once as an ethernet device. Then, I use the IR Power On command to turn it on, and the ethernet commands for everything else. Been working well thus far.
However, the keyboard command doesn’t seem to work. I’ve tried it in several different text entry fields on the device, and typed characters never appear. Is this one of those abilities that isn’t available until you register it with Sony’s Media Remote iPhone app (the one that currently won’t find Series 10 devices)?
On a completely unrelate note, if you press Play while a video in the YouTube app is already playing, the device stops responding to inputs and you have to pull the power cord to restart it. I assume this is just a bug in the firmware/youtube app.