Orbot:
However, Orbot captures all network traffic system wide and enters it into the TOR network on the device itself. There are disadvantages to this method, as opposed to the traditional method of configuring each application to talk to a TOR proxy.
The advantage is this will run all network requests through the TOR proxy, without each application having to negotiate a connection with the TOR proxy. Implication being support for more applications since they can make requests as usual, and less chances to accidentally send out something without going through TOR.
The disadvantage is everything will run through TOR, without each application having to negotiate a connection with the TOR proxy. Implication being it’s harder to choose what to run through TOR, or use TOR with a VPN, either nested or selectively for some applications.
More importantly, it makes it harder for TOR to isolate different applications to different circuits, since it doesn’t get to know the applications individually*, and since the network is only concerned with where to send packets instead of what’s actually in the packet, it would be harder to put different sites on different circuits especially if they’re all coming from the same browser, or the browser be able to talk directly to the TOR proxy to make requests such as changing the circuit for a specific site.
*The way mobile OSes put each app in their own user actually makes it possible for the VPN application to tell which application the traffic is coming from.