If the case is going to an engineering shop that has good inspection facilities, then they should be able to measure & record a good endplate hole centres by which to work to. In fact, if any OEM blueprints exist for either the endplates or cases, that would be extremely useful for the LCGB to have on record......
In any case (excuse the pun

) with the critical dimensions obtained, the engineering shop should be able to correct any misaligned/oversized holes by deeper drilling. Personally, my preference would be to fit hollow dowels/sleeves in the correct dowel positions to take OEM type 7 mm (check that!) dowels & Helicoil inserts for the M7 stud holes.
To answer your question, there is no issue with stepped dowels apart from my own reluctance to use stepped fastenings such as studs. Stepped studs as marketed by some have no certainty of correct strength, whereas OEM studs are of the correct quality &, of course, longer M7 studs intended for the cylinder inlet can often be utilised in place of the shorter endplate fixings. I have often done so with damaged cases as well as inserting M7 Helicoils in dire cases.
For the record, prior to obtaining M7 Helicoiling kit I tapped out some slightly baggy endplate stud holes with an M6 Helicoil tap (same pitch) & fitted Holokrome/Unbrako/GKN high tensile M6 SHCS's & it was fine. There is often some cynicism associated with Helicoils, but the fact is many manufacturers - Rolls-Royce included - fit them during manufacture to stressed alloy components.
I hope that information helps.....

Edit: Having just re-read your last post, the fact that you await a 'new endplate' concerns me, if it's anything like the majority of remade components. I'm surprised you haven't a selection of spare endplates (it doesn't need to be OEM Spanish, though they are as good as OEM Italian). I wouldn't trust the Indian endplates for accuracy. If you need an OEM Innocenti endplate, I'm certain I could spare one.....