UserAgent: Mozilla/5.0 (X11; Linux x86_64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/59.0.3071.115 Safari/537.36

Steps to reproduce the problem:
1. Add --incognito to ~/.config/chromium-flags.conf
2. Install a Chrome app from store, and create shortcut from the Apps page in a new (non-incognito) tab
3. Launch the app from the system's applications menu

What is the expected behavior?
Since apps cannot be enabled in incognito, Chromium should ignore the --incognito flag in chromium-flags.conf and launch the app.

What went wrong?
Upon opening the app, a new icon/text is created in the taskbar, with the name and icon of the App that was launched, but after a few seconds, this disappears. No actual chromium window is created.

WebStore page: Any Chrome app - tested with Google Keep and Chrome Remote Desktop

Did this work before? No 

Chrome version: 59.0.3071.115  Channel: stable
OS Version: Arch Linux; kernel v 4.11.9-1
Flash Version: Shockwave Flash 26.0 r0

--incognito is the only option I am using in chromium-flags.

The .desktop file created by chromium used --app-id=<app-id>. I tried changing this to just --app=<>, but this just results in a new empty incognito window opening (as described in this issue: https://bugs.chromium.org/p/chromium/issues/detail?id=167802, which seemingly has regressed again).

Launching the app from the browser itself (by opening a non-incognito window, going to the Apps page in a new tab, and clicking the app) works fine.