Spraying vs wipe on vs brush will only make a minimal difference. Even surface prep is a big part of what will happen. Honestly, going to 320, especially on a hard wood like WO is probably too fine. At this fine of a surface then the variances in the density of the wood will show more prominately, ie possibly blotchy. With a rougher grit, you are creating more places for the stain to reside and the color of the stain will be stronger and more even.
I'd wet the suface and let it dry, then do a light sanding with 150. I know is seems sacreligious (sp?) but you will get a better more evben tone. Just add a few more coats of the final finish and it'll flatten out just fine.
Also, my experience with water based stains is that I like to really sloch it on and grind it into the suface followed by almost buffing it out to relly get it even.
WO should not be generally be blotchy.
If you could match the color sufficently, you could go with a premixed NGR stain. Once the alcohol is gone, you can go water based over it. It will give an even color on anything (in my experinece). However, lapping marks are hard to avoid so it's kind tough for big surfaces. Although I do it and just feather in any lapped areas with another wash of stain. You can get this from the nice folks at Wood Finish Supply.
BW