I would use one temp reading device and not worry about comparing. If you look at the specs, they are often accurate to plus/minus 2 deg C over the range. That means plus/minus 3.6 deg F. That is a large variance over the entire range and can translate to some variation at any one temperature. If you wanted a thermometer accurate to .01%, it would cost $300 easy.
When you have a probe taped to Flexwatt, you are sensing the average temperature of the heater plus tape plus air space around the probe. The smaller the probe, the closer the actual temp of the device being read. And probes can be affected by airflow, etc.
For infrared thermometers, the emmissivity of the object (reflective/absorbtive property) affects the reading.
Also, if there is an air space under a portion of the Flexwatt, a probe may register a slightly higher temp at that point. Understand that Flexwatt only provides so much power. Even a 100 deg F spot will not hold 100 deg F once touching a box and spreading the heat energy out.
So, it doesn't matter. Reptiles move around to adjust their internal temperature. If you give them enough temp range and enough room to thermoregulate, it doesn't matter if the heat tape is 90 or 88 or 95 or whatever. Racks limit both temp range and room, that is the problem. If the snakes avoid the warm area, turn down your temperature controller a bit.
Also, if you really want to see a stable temperature, measure the temp of a thermal mass over the heater. That is, measure the inside of a box with substrate over the heater. That scenario is less subject to variation than measuring the heater itself.
Covering the heater with sheet metal (aluminum sheet is best - get it at smallparts.com) increases thermal mass and makes for a much more stable temperature.
-----
Mark