While they may be lobbyists for the engine manufacturers EMA doesn't have any financial interest in whether or not you pay road taxes; therefore, it is unreasonable to ascribe sinister motives, to their B5 recommendation, for the purpose of supporting collection of road taxes.

I doubt they have any financial interest in what type of fuel you burn, since they don't sell fuel; however, they do have an interest in the way the fuel may affect an engines reliability.
If you carefully read the literature they've put out, on the topic of BioDiesel, you'll find that the reason EMA doesn't endorse the use of anything higher than B5 is because there are no standards that cover B100 or Bio/Petro blends over 5% Bio (B5). There are two existing standards one covers Petro diesel and the other covers Bio that is suitable for blending with Petro. A blend of 5% standard compliant Bio with Petro also happens to meet the existing standard for unblended Petro so EMA endorses its use. Once standards are developed and thoroughly tested for higher percentage blends it will be in EMA's best interest to endorse those blends