It has long been the case that intentional draws are reported 0-0-3, and MTR 2.4 states as much. In the most recent update to the MTR, the release notes said

We have clarified that you can also use the “0-0” result button in Wizards Event Report (WER) to enter an intentional draw. This will automatically enter a result of 0-0-3 for that match.

However in Appendix A of the MTR (changes from previous versions), it states

Drawn games are reported 0-0-1 or using the draw button.

And using the “0-0” button in WER does indeed report the match as 0-0-1. What's going on here?

The reason we added the original note about reporting IDs as 0-0-3, was because people kept asking. But the software never complied with the stated policy; DCI Reporter, the precursor to WER (and WLTR) also had a 0-0 button, the mouse-over text specified it was for IDs - and it recorded the result as 0-0-1. WER (and, I believe, WLTR) also default to 0-0-1.

And, once again, people kept asking - so Appendix A now clarifies that you can manually enter 0-0-1, or use the draw button, and be in perfect compliance with policy.

I'll note that, as long as you were consistent within a tournament, it didn't matter whether you recorded 0-0-3, 0-0-1, or 0-0-9. Other than a highly infrequent corner-case, it didn't even matter if you weren't consistent within a single tournament - the real effect on tiebreakers was nearly non-existent. However, an answer of “I don't care” never satisfied people asking “how MUST it be recorded?!”, so we settled on an answer that's as good as any other; now, the answer's updated to more closely match what the software does. (At least, until some future update; I can't make any promises…)

d:^D