The pre-stain will help somewhat, if the color is too light then you can re-stain with the same color. A darker stain will make the blotches show up more. Staining will accent, not hide any mill marks so if you want a professional looking finish you will have to sand, probably up to 320 grit if you do not want to see any swirl marks from an orbital sander.
The big boys will completely seal the wood and let it dry then spray light color coats without wiping until they get the color they need, yes the grain is obscured but they get an even color without blotches. You can do the same by brushing on the stain and not wiping it off, I have seen alder doors finished on site this way and they looked great. Minwax is not my favorite stain, I prefer Sherwood stains, they have more pigment and a faster evaporating solvent.
Water based stains do not get as blotchy as oil based stains but you have to be quick and still use a compatible stain controller too.
And the doors you already stained - you might have to sand them back down to bare wood and re-stain the same as as the rest of the doors or they will never match.
Wayne