Error updating temporal tables
Is this something that will always need to be handled in an exception routine? 


The system generated start and end times are keyed to the server's system time at the moment the BEGIN TRANSACTION is executed.  If you have long-running transactions, you should:


Build in exception handling that can retry the transaction.
Rework the offending code so it executes more quickly.  This may sound like a lot of work, but it will be necessary to do some level of rework to handle temporal-based exceptions correctly.  If you're going to do rework, you may as well determine why the transaction is taking so long, and mitigate that behavior.



  Or is Microsoft considering to change that behavior?


There is no way to know what Microsoft will do in future versions of their products unless they have made a public announcement that is not covered by a nondisclosure agreement.  They might modify the temporal table functionality at some point in the future such that the start and end dates are reflective of the current system time at the point of insert/update, however that is not currently how it works.