I think you are confused with the terms Point to Point and TR-069 here.
An ISP normally uses IPOE/PPPOE/PPPOA for establishing the connectivity between CPE(Modem/Gateway) and their BRAS. They also use their own radius server to authenticate the PPP connection for obvious reasons.
TR-069 is a mechanism to provision a Gateway/Modem with the respective plan(End customer plans based on their chosen plan) and other operation from the network operator point of view.TR-069 also can be used to fetch the complete data model of the Modem and operator can pretty much read and write(only Writable Parameters) from the CPE.
In addition to this,ISP will also set a periodic inform counter in which CPE will also send periodic Inform with information such as Model number,Software version and other details towards ISP's ACS(Access Control System). This is how ISP understand the firmware version of the CPE and trigger a Software upgrade on a scheduled basis.
TR-069 can also be used for ISP to trigger Remote Procedure calls where CPE will trigger WiFi Scan,GET,Set, etc operations.
On a layman perspective, PPP is L2 protocol and TR-069 is an application layer protocol.
I will be more happy to provide more detailed answer for any queries regarding CWMP or TR-069.Let me know if you need more info on this.