I'm not sure what an "external e-ticket" actually is - perhaps a paper print out? I think the whole point of a chip card is that QR codes are irrelevant, like Oyster over here. I'm GUESSING what they mean is an electronic receipt/email confirming the purchase (and apparently not a paper receipt, and certainly not a bank statement or similar). But last time I tried, it seemed impossible for a non-resident to obtain a chip-card version of the D-ticket anyway. (The chip card also only seems to be available via a small handful of providers).
I don't think the OP has much to worry about as long as they are going to use an app. At present I see HSB say they cannot offer the D-ticket subscription themselves, so you HAVE to choose a different provider.
This was checked several times as I went Wernigerode - Eisfelder Talmuhle - Quedlinburg, and accepted without question. I'm guessing they scanned the QR code, though I can't remember specifically.
Wandering Pom describes very much the experience I would expect. Personally I have the Vehrkersverbund Rhein Moselle smartphone app version of the D-ticket. All DB ticket inspections have involved a scan. All bus drivers have always just waved me on without a scan, including buses in Bavaria which are way off-patch for VRM
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I am rather surprised that they cannot read chip cards as they are very common in Germany.
All german bus operators I have dealt with offer an app, and give QR/Aztec codes even for single tickets via the app.
I'm also inclined to think that it's their problem if they can't read one of the agreed ticket formats, and not the passenger's problem.
I'd be careful here - I don't think HSB are required to accept the D-ticket at all. They may be doing it out of the kindness of their (shareholder's) hearts.