Certainly not a dumb question at all. Both are going to raise the bike in the rear, but by different methods with different side effects.
The dogbones would be most applicable to someone who finds the existing spring appropriate for their weight/loads, but wants better cornering clearance and quicker handling. Basically, you are going to be changing the handling and cornering clearance, but leaving the suspension the same.
The spacer (and/or simply leaving the preload lever on 'Hard') would be more appropriate if you're carrying a heavier load and need to firm up the springing at the rear. More preload is basically a shortcut to having a spring with a higher rate. But it will also help cornering clearance and qucken the steering.
To be scientific, you should measure the sag on the bike, both unseated and seated. If you use about 10% of the available suspension travel unseated, and 30% seated, then the spring rate is generally correct and the dogbone approach would be best. If you are getting too much sag, then preload (or a new spring) is the better approach.
All this is the theory, but for me, the big problem with the FJR is cornering clearance - it is the achilles heel of the bike as I ride it. I've done the spacer and might do the dogbones too, just to try and get the footpegs off the tarmac. Or now that I've nearly 10K on the bike, it might be time to stop dicking around with band aids and do the right thing - get a new ride-height adjustable rear shock. I'm partial to Ohlins because of good experiences on other bikes, but a lot of folks here like the Wilburs.
- Mark