This can now be done with Chrome 79+. Thanks to the Reddit link from @Kropotoff's earlier answer, vous pouvez restore the "Always open these types of links in the associated app" option by updating your system settings.
For Windows:
Apply the "ExternalProtocolDialogShowAlwaysOpenCheckbox" registry policy
Or edit le registre and add a REG_DWORD registry entry to:
Software\Policies\Google\Chrome\ExternalProtocolDialogShowAlwaysOpenCheckbox
For macOS:
defaults write com.google.Chrome ExternalProtocolDialogShowAlwaysOpenCheckbox -bool true
At least on Mac, it seems vous devez quit and restart Chrome before the option becomes available.
Another Method
As an alternative to enabling the checkbox, then launching Chrome to select the checkbox, and ensuring it is persisted in the Chrome profile, it also appears to be possible to whitelist specific protocol handler URIs via the ligne de commande. This is helpful for Selenium and other automation, meaning that the URIs open without user intervention and you don't need to pre-configure the browser.
Assuming that your protocol handlers are myprotocol1://whatever and myprotocol2://whatever, vous pouvez do this on Mac. If you go this route, it doesn't look like vous devez bother with the checkbox setting above.
defaults write com.google.Chrome URLAllowlist -array 'myprotocol1://*' 'myprotocol2://*' 'myprotocol3://*'
The name 'URLAllowlist' is supported from Chrome 85 onward and it is required for Chrome 100+; earlier versions of Chrome (15-85) also supported 'URLWhitelist' in place of 'URLAllowlist', but URLWhitelist was deprecated and then removed.
J'ai not tried this on Windows, but it looks like there is guidance on the enterprise policy page for URLAllowlist.