After some extensive testing I noticed the following issues:
-Altitude registered by Piksi is 30+m off ublox due to different frame of reference, leading to arming checks issues.
-If connection is intermittent it does not skip to the latest observation but process them sequentially in a queue, as a results the location information is delayed which is very risky when flying with a drone, the effect is that if ekf switches gps the pos goes mad and projects way ahead, overshooting the target heavily, and causing a flyaway.
-RTK Float can degrade significantly without changing gps status, therefore even if you have 2 gps ardupilot sticks with it.
-HDop self- logging of Hdop is heavily different from ubloz with hdop close to 2.1-2.5 when there is rtk fix whereas when in SPP there is much lower Hdop values
-No heartbeat from piksi messages received when piksi transitions to no fix mode(intermittent behaviour unknown origin).