No, I think you would have to restart the Wii to gain control of the controller.
I haven't tried any of it yet...I'm still waiting on the bluetooth dongle. So everything I'm thinking of, besides viewing all the uTube videos, is pure speculation. A guy at work has tried using the Wiimote just to controll the computer as a mouse for fun, and using GlovePIE, and he's the one that indicated the sync issues. Now thinking, I don't remember if he said it would sync to the first-come/first-served bases, or if the Wii powers on, it assumes control of the controller regardless. He said it worked great.
The nice thing is that there are already a couple of Wiimote scripts with the GlovePIE download that will get you going with basic funtionality. I'm going to look at it more and see if the scripts can be written to send xsend commands. That would at least give you tight, yet basic integration with xlobby. Then get it to work with Girder for complete control like you said...though looking around, I'm not sure a plugin for girder exists right now.
*EDIT*
Just viewed a video that indicated that the player was ~400' (most likely ~100 feet...it makes more sense the way the fat guy runs...as one comment...there's no way he ran 1 1/3 football fields in 10seconds) away and still was able to bowl. Mind you it was still in a line-of-sight between controller and console.
*EDIT yet AGAIN*
Two comments from that utube video:
I believe it, my friend went everywhere in his house while I reported Wii response form the basement (in Zelda).
He couldn't find a spot in the house it wouldn't work in, that is through at least two floors and walls plus the distance.
tried this in my house (which is a fraternity, so lots of rooms and stuff in the way between walls) and I was able to get it to work from 100+ feet away.