While WotC could reject any d20 license, the only times they did were abuses of their morality clauses, AFAIK. Had they mandated some rules adherence it might have been different. That gave d20 something of a poison pill: in the beginning everyone was desperate to be completely 3e compliant to get the most share of the flash market.
Afterwards people started diverging, typically in products that were competing with WotC. E.g. Mongoose's Quintessential x was competing essentially with WotC's Complete x (though it would be more precise to say Quint was competing with S&F, T&B, etc) and the settings were fighting with the 3.x FR and Eberron.
Divergence worked in WotC's favor as it caused market fragmentation and the devaluation of the d20 licence. After about the 3rd year, people started losing confidence in d20 products being compatible with D&D. There was a resurgence with 3.5 but the honeymoon was relatively brief as people again became disenchanted.
IMO the M/R/SRD publishers & the Open Gaming Foundation should get together and make up their own logos to reflect the rules in use and if it is a strict adherence or not. The licensing terms, IMO, should only be based on whether the supplement actually adheres to the xSRD rule set or not. If the product rewrites core mechanics it would have to use a "Variant" or "Alternate" logo, as would any supplement that relies on an SRD variant rule set.
This would mainly benefit settings and books covering mechanics not addressed in the SRD. Alternate rules are probably the largest number of products which will, as usual, get little benefit from the d20 logo.