Hi @VipulSparsh-MSFT and @Walker McAninch , I managed after some lengthy testing, to get to the bottom of the problem for us. I did try older versions of Windows 10 (1903 etc.) and this wasn't the issue. We use Chrome CIS Level 1 security benchmarks that use ADMX ingestion (Chrome ADMX). One of those policies (which is now deprecated by Google) - NativeMessagingBlacklist with a wildcard (*) blocks access to the Native Messaging API's. You can either add in NativeMessagingWhitelist with your exceptions or use the newer Chrome policy of NativeMessagingBlocklist. This policy was the problem though.
This was the original problem setting within Intune in the custom OMA-URI format with no whitelist set:
./Device/Vendor/MSFT/Policy/Config/Chrome~Policy~googlechrome~NativeMessaging/NativeMessagingBlacklist
<enabled/><data id="NativeMessagingBlacklistDesc" value="1*"/>
Once this policy was updated to the new version or a whitelist entry added for the extension for the older policy version, it worked.
EDIT: Please note that the above NativeMessagingBlocklist and NativeMessagingAllowlist are only supported in Chrome 86 and onwards. To use the legacy policies, add the following Blacklist and Whitelist in:
Legacy Blacklist Policy
Name: <Your custom blacklist policy name>
Description: <Your custom blacklist description>
OMA-URI: ./Device/Vendor/MSFT/Policy/Config/Chrome~Policy~googlechrome~NativeMessaging/NativeMessagingBlacklist
Data type: String
Value: <enabled/><data id="NativeMessagingBlacklistDesc" value="1*"/>
Legacy Whitelist Policy
Name: <Your custom whitelist policy name>
Description: <Your custom whitelist description>
OMA-URI: ./Device/Vendor/MSFT/Policy/Config/Chrome~Policy~googlechrome~NativeMessaging/NativeMessagingWhitelist
Data type: String
Value: <enabled/><data id="NativeMessagingWhitelistDesc" value="1com.microsoft.browsercore"/>
The important value is the com.microsoft.browsercore value above. Be careful when copying and pasting the "Value" data above in respect of the speech marks ("") as if they are wrong, you'll get a remediation error within Intune.