Take at look at the bleed location?

This is stock from the factory. Isn't it at the wrong end of the caliper? The bottom instead of the top?

 

That's a different calliper from what I have, are you sure it's stock? And you are correct the bleed screw should be at the top. I don't know what else to tell you.
It looks like those are two piston calipers.
What year and model is your bike?

 

Any chance that they are upside down and on the wrong side?

 

Given that Yamaha was very good about using the same castings on multiple machines it may be that you have a pair that were used on something else that required the bleeder to be in that position, and the caliper to be oriented 180º from where it is now.
For example the FJ600:

 

Nope. They wont' fit that way and still have the pads over the disc.

On the X the bleeder is supposed to be at the end with the mounting boss that is furthest from the piston.

 

!985 XJ700X: I have owned it since new. 11530 miles. No work has been done on the brakes. I started trying to bleed the system and found the situation. All the photos of for sale used are like k-moe's photo. If it can be bleed I can use it otherwise replacement. A new master cylinder started the work. I have found the pad backing plates have rusted and the whole thing needs work.

 

Just remove the calipers to belle them. Place a block of wood between teh pads and orient the bleeders so they are the highest point.

Replace the brake lines while youre at it.

Somebody at the factory grabbed calipers out of the wrong bin when they built yours, or someone at the dealership goofed big time during set-up.

 

I am going to put them in a bleed up position to bleed after I get them in working order.