Why do temporal tables log the begin time of the transaction?
The idea is to track logical time vs physical time. Logical simply refers to what a user/app expects the time of an insert/update/delete to be. The fact that the DML operation may take a while for whatever reason, isn't meaningful or even easily determined and understood by a user. If you've ever had to explain lock vs latch contention to an accountant (I have), it's a comparable situation. 

For instance, when Bob "tells" the app that all employees in Bob's department will start making $42/min at 20160707 11:00:00, Bob (and his employees) expects everyone's pay is now calculate at $42/min from that time. Bob doesn't care that for this to be effected, the app has to make 2 reads and 6 writes across the database per employee and their data + log files sit on a bunch of RAID-5 SATA II drives so it takes about 7 minutes to finish the task for all 256 of Bob's employees. Bob, his accountant and the payroll manager care that all his employees are paid $42/min starting 20160707 11:00:00. Else, the employees that were updated at 20160707 11:00:01 will be slightly annoyed while those whose records were updated at 20160707 11:00:07 will be gathering outside the payroll department.

There are valid use cases to track physical time such as debugging and forensics but to the end user, it's generally meaningless. The Tlog keeps both ordering and timing information for each of the write operations (among other things) so it's there if you know how to look.