Not sure I quite fully understand you. 0x5e is indeed the default value, corresponding to a threshold of 4.208V. The 4.16906 is likely what the cell voltage actually settles to after it stops charging. The values in upower currently only seem to show the current voltage, not any set thresholds.
Now that I think about it, I suppose it shouldn’t be too difficult to patch the kernel to add sysfs files for these settings that could more safely and easily set these values and read them back for use in upower or similar (if it even has any kind of support for reading charge thresholds). Maybe I’ll have a go at that at some point… certainly not today though.