I went back and forth with support for a while on this with no definitive resolution – though they said that they were working on an update for powermatch to try and correct this issue. In the meantime, they recommended that I just use the trainer to control the power, since my Kickr and pedals were reading within a few watts of each other.
As others have suggested, it does help to try and keep your cadence and pressure to the pedals as smooth as possible. This results in the trainer trying to “self-correct” less which leads to smoother power.
That said, even when I do that I find that the intervals can still be off by 3-5 watts. For example, when using the pedals and powermatch an interval target at 280 watts might end up with an average of 276. Despite this, like you mentioned I never really felt a difference in the resistance level, so I am not sure it actually has much of an impact on the training benefit.
Let me know if you hear anything different from the support squad.