OK, I should have emailed Christopher of T3 Technique first about this, I did late last night and here is his response:

Hmm, so you have one grease cap that is larger (longer) than the other? That would mean that you have a mix of components. The "tall" (approx. 10mm taller than the "normal" caps) Vanagon grease caps are pretty rare and it is not normal to have two different sized caps. The short caps make life a lot easier, so I would suggest ordering a new drivers side cap from Van Cafe or simply cutting 10mm off of the end of your existing cap. You will lose the lip that aids in the cap's removal, but it will still function just it it did before, only shorter. You will have to push the speedo cable further into the spindle by a like amount.

So, it appears there is a grease cap that is taller, and for whatever reason my van ended up with one.

Jeff Stewart