From the 6.44 beta topic:
What’s new in 6.44beta6 (2018-Sep-11 08:52):
…
*) ike2 - fixed rare authentication and encryption key mismatches after rekey with PFS enabled;
So if you can afford to dedicate a device for testing the 6.44beta6 against strongswan, it would be great. I’ll do that on a pair of Mikrotiks in a few days, currently they are busy testing something else.
The sooner the fix is proven to be stable, the sooner it can be backported to 6.43.x.