It is reasonable, but I can say the author has been a bit lazy not to take the input colour profile gamma into account, because doing so is quite simple once you know the colour profile in which the image is encoded. In fact a proper way to work on tone mapping algorithms would be in a linear space (gamma=1.0) which would in the end be reverted to the desired output colour space's gamma. Anyway it should be simple for you as well correcting those darker images with an additional gamma-type curve.
Basically what happens here is that SNS-HDR is surely focused on getting a certain histogram distribution, but the same RGB values will render darker or lighter depending on the gamma of the colour profile used:
These three histograms correspond to the same image, with the same appearance on screen:
Since ProPhoto RGB's gamma is 1,8, the histogram gets lower levels than when represented in sRGB (gamma close to 2,2) or Adobe RGB (gamma 2,2), just look at the position of the blue peak.
If SNS-HDR's algorithm tries to produce a given histogram distribution, it will render lighter in ProPhoto RGB than in Adobe RGB because
a similar RGB combination corresponds to a lighter colour in ProPhoto RGB than in Adobe RGB.
Example: RGB levels for different gray tones:
Regards