Issue with HW CTRL flow on ttyTHS1

Yes, it should be expected since JP5.x and JP6.x have some differences in device tree for the numbering of UART interface .

Yes, they are expected that RTS would pull low when it is busy and turn back to high when it is idle.

Are you using Uart interface for RS-485 so that you want the opposite behavior?
If so, you can refer to Need to Invert UART2 RTS - #5 by KevinFFF for this use case.