Can you be more specific about which templates and class variants? Unfortunately, there isn't a way to affect all templates/variants to fix issues like this. It will have to be done on a case-by-case basis.
It doesn't look like a specific variant, but an issue with the scripting for variants as a whole. If you select variants that replace bonus feats, only one of them seems to work properly. The additional ones only shift the bonus feat.
I noticed this when I was making the changeling egoist substitution levels. Two of the three (levels 1 and 5) replace bonus feats but instead of replacing both feats the changeling would still get one of them. At first I thought it was something I was doing but I tested it with the fighter variants and had the same result.