I fitted new rear pads and a fancy titanium caliper pin (as the OEM version rusts) and thought I'd complete the job by bleeding the rear circuit. The actual bleeding process was straight forward, but I made a little error that was pointed out by my kind Yamaha tech today.
 
When you remove the filler cap, there is another plastic lid with a rubber seal underneath. If, like mine, it hasn't ever been removed before then there will be a small vacuum under the cap and the black rubber underneath will get pulled into its elongated version.
 

 
I just presumed this was its natural position and put it back this way. However, this really limits the amount of fluid you can have in the reservoir before it spills out of the top when you put the seal back on.
 
You should push the seal back into its compact position with your finger before refitting.
 

 

 
You can now fit more brake fluid in the reservoir and should be able to see through it clearly.
 
Apologies if this was bleedin' obvious (see what I did there with the pun? No?) but it may help someone.

I enjoyed the pun.
 
Thanks for sharing!

"Bleedin' obvious", like the pun.
 
One other tip when installing brand new pads, that should be when your fluid level is at "full". As the pads wear, your pistons get further extended and more fluid is displaced into the caliper from the reservoir.
If you fill the reservoir when the pads are worn, you will have a hard time retracting the pistons back into the caliper the next time you replace the pads.

Hello reservoir. Is that your diaphragm or are you just happy to see me?