Requested on r/macapps: comment
Show notes instead of notes.md in the sidebar, so the file list reads like a list of notes rather than filenames.
Where it stands today: shipped in 1.0.1. See the reply below.
Shipped in Inkstone 1.0.1 
Turn it on in Settings ▸ General ▸ Sidebar ▸ Hide .md extensions. With it on, notes.md reads as notes in the sidebar (Pinned too), in tab titles, in Quick Open and on the start page. Renaming shows the short name and keeps the file a .md file.
It hides Markdown extensions only. Folders keep their full names, and other files keep theirs (notes.txt, photo.png), so two files never end up with the same name in the list.
1.0.1 is out now for the direct download (Inkstone ▸ Check for Updates). The App Store update is coming soon.