Rockchip has 10-bit H264 support, lacking on all Amlogic devices.
RK3399 also has more display output ports and Linux support is generally better with already working open-source GPU drivers.
Rockchip Android Pie also supports HD Audio passthrough missing in most Amlogic devices.
Amlogic is generally cheaper and the latest S922x chipset is faster than RK3399.
But next year there will be a new RK3599 processor that will run a 4K UI compared to all devices that still run a 1080p UI, with only 4K video playback actually running in 4K.
The biggest problem for Linux is mainline kernel support for devices and the AP6398S wifi chip that has no mainline drivers, used by both Amlogic and Rockchip and other vendors.
If you use Linux - Rockchip RK3399 is better, if you only use Android then Amlogic S922x will be cheaper and faster. But Android software support is basically the same for both chipsets.