Very interesting theories you got there.
I highly doubt they will auto-ban you if the "bot-meter" fills up.
They have a special section for these type of investigations, and must be done manually.
Initially its the same thing.
Only difference is that a VPN allows you to change your IP for all traffic coming from you computer.
A Proxy can be used/set for 1 program, so it won't affect other software running on your pc.
More info at Proxies vs. VPN - What's the difference? - BestVPN.com
PS...
It does not make sence tho how Jagex handles bans lol.
If they manually ban you, you receive 48 hours.
[As if they aren't entirely sure]
If BotWatch bans you, its perm ban.
A player could have reported you.
Sorry to hear that buddy :(
48 hours ban are manual bans.
This means a J-MOD spotted you botting, and banned you instead of the BotWatch.
[BotWatch is the automated Bot Detection system Jagex created]
Using a proxy has several advantages.
If your own IP is flagged and you wish to use a new one
If you bot on multiple accounts and don't want all of them banned when one gets banned. [multi-ban] [gold-farming]