Can thinned water based polyurethane be used for blotch control?
In a word: no. Okay you can in theory, but there's no guarantees. There are three schools of thought when it comes to conditioning. 


Flood your conditioner on, wipe off the excess, and then stain before the solvent (water in your case) dries. 
Apply the conditioner evenly, repeatedly reapplying as dry spots appear until you have a perfectly uniform saturation, then let it dry overnight. Once cured, scuff sand very carefully to remove and conditioner left of the surface. Then stain.
Shellac. Don't worry about shellac, it's a whole other bag of problems.


To do number one you would have to introduce more water into the wood than I would say is advisable, more water = more grain raising, more warping, and the finish may start to fail to bind together which would completely defeat the purpose. Not to mention water dries so quickly you'll have trouble keeping things in solution long enough to work properly if it's a big piece.

You could in theory shoot for number two, but it is a technique that takes some practice and you'd be adapting methods from the world of oil based to work with water-based products which will take some experimenting. Basically you'd need to find just the right amount of dilution so that your poly behaves itself, in oil based it's about 2 to 1 mineral spirits to varnish (typically).

To be honest, this is kind of a lot of time and effort to avoid buying a $20 can of conditioner and your results will be far from a sure thing. Here's an article on conditioning with an emphasis on water based products that may help sell you on the benefits of a true conditioner. Wood Whisperer. Good Luck!