The password is stored in secure storage by the UI in order to increase. That said, the proxy passwords will still be loaded from the .conf files if they are defined.
I think the best way to address this is by defining your proxies in website_monitoring.conf as documented here: https://lukemurphey.net/projects/splunk-website-monitoring/wiki/Using_multiple_proxies.
Make sure to add proxy_user and proxy_password to the website_monitoring.spec file (that isn't shown in the example in the link above, but it is supported).
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