Sorry, my point was probably not clear. I mean, task markers should not been converted but just displayed in TaskPaper window as appropriate bullet characters or maybe checkboxes.
Honestly, I don’t see this as problematic. Considering quite a lot of existing applications hiding/interpreting explicit user markup (e.g. Org mode with org-bullets, Dynalist, Typora, MarkText, etc.) and discussions here, here, and here, I think this would not lead to much confusion for users. (Of course, this behavior should be documented in the User’s Guide.)