Shawn Sijnstra was kind enough to supply a NEWDOS/80 Zap from Northern Bytes Newsletter which will correct the usage of the CLEAR command.
Unzapped, the CLEAR command does not honor any HIMEM setting. Tony Domigan developed a zap for the Model III which would cause the CLEAR command to clear from 5200H to HIMEM instead of 5200H to FFFF. Using the command CLEAR * will clear to FFFFH.
The added zap can be found on the Unofficial NEWDOS/80 v2.0 ZAPS page.