In both scenarios, compromising Chrome in one app qube won’t affect Chrome in the template (if it exists there) or in other app qubes. However, scenario A is more standard. With scenario B, you’d have to install and update Chrome in a non-standard way.
No, because qubes are securely isolated from each other:
Unless you mean that Chrome in the template becomes compromised via a malicious update, for example. In that case, yes, all instances of Chrome based on that template (including the one in the template) would be compromised, but this doesn’t break the security model of Qubes itself. Qubes is still doing everything it should be doing in this scenario, because Qubes doesn’t claim to be able to prevent malware from being installed in a template (or any qube). All it claims to do is contain the damage by keeping qubes securely compartmentalized. In this scenario, the damage is still contained in the sense that other templates and other qubes based on those other templates remain unaffected.