Yes Tor is used for all communication by default. The Bitcoin network part you can deactivate Tor if wanted in the settings. But default is on.

Webpages might block access via Tor bc cybercriminal might use it for DDoS. Not sure about that... I assume main reason is that they cannot track users and therefor generate revenue by collecting user data. Big data is a big business and should be called Big Surveillance.
In our case we use Tor hidden services. For the Bitcoin network we mix hidden services and plainnode full nodes so risks with exit nodes are limited as well.