I am adding an Application Catalog Rule for Google Chrome and in the Advanced tab I am configuring the Home Page and a managed book mark. It works without issue.
I also have a Profile Configuration Payload for Webfilter - The web filter blocks * (all sites) and allows the end user URL only.
Depending on which element gets assigned last is what works. It appears the two cancle each other out.
For example if Chrome is updated by Google Play the settings work but then as soon as the web filter is applied the home page and managed bookmark are gone but the web filter works.
If the web filter is applied first, it works great and all sites are blocked but as soon as google play applies the chrome with config the web filter stops working and you can brows anywhere.