I 'think' TT are redirecting DNS, but they are at least offering a way to opt out. Unlike BT, they dont appear to be sniffing out and redirecting port 53 traffic.
With not being a customer I cant check, but everything Ive seen would seem to indicate that their DNS servers are simply using BareFruit services. So the opt out is an easy fix to change to one of their DNS servers which isnt using Barefruit. ISP's usually have a whole stack of DNS servers. I think at one time I counted that BT had in excess of about 20 so Ive no idea how many TT have.
Im only guessing but they could have things set up so that say 2/3rds of their DNS servers use Barefruit, whilst the remaining 1/3rd are 'clean'.
Then its likely that their opt out solution reconfigures your modem to set the DNS server to one of the 'clean' servers. The problem with this though as you pointed out, is that the change does not survive a reboot.