If you look carefully at the free version of the DUC/DDC compiler provided with Vivado you'll see that it is not general purpose. It is targeted to the cell phone industry (LTE/CDMA) and does not have the bit widths, clock rates and decimation factors needed by the Kiwi.
The Kiwi does take advantage of some Vivado IP blocks, like the DDS compiler. And it makes very heavy use of the Artix DSP blocks to save FPGA fabric gates. We also wanted to have a design fully independent of any FPGA manufacturer's architecture in case we need to change devices in the future. It was also a learning experience for us to implement everything from first principles.
v1.172 adds a switch to the admin page GPS tab called "include alerted?" that overrides the exclusion of alerted sats from the position fix. The alert "A" symbol will appear green instead of red when the sat is actually being used. It will be interesting to see if some position fixes get worse when alerted sats are included.
GPS alert flag: There was a late change that went out after the initial v1.171 release. Most of you will have picked up the change. But if not, force an update by clicking the "build now" button on the update tab of the admin page.
As shown below if a satellite has the "alert" flag set in any subframe a red "A" will appear where the yellow "U" normally appears when the tracking PLL is unlocked. As of this writing PRN 195 has its alert flag set which is reflected in the outage status messages published here: http://sys.qzss.go.jp/dod/en/naqu.html
When the alert flag is set the satellite data will not be used in computing a position fix even though subframe data is decoding properly.