I compared all three (using Fuji RAF files) and the only difference I see is that using it as a Standalone gave that rather pale result that others have seen compared to using it in LR or going from LR to PS and using it there (and saving it back to LR). If you use it having opened in Photoshop you are likely using it on a dng file as that's what LR/PS uses internally but when you come to save the denoised file it has to be a new file (so again a TIFF file or one of the other available image file formats (but I don't think dng is available)
If you use it from Lightroom you have to create a TIFF file because Lightroom can't store the denoise edits in an XMP file as it does with its own edits. If you use DeNoise as a standalone on a raw file from the camera it must handle the demosaicing internally and it will let you save the result as a DNG - leaving the original raw file untouched. One consideration is that Topaz DeNoise can never actually do anything to the raw file as it comes out of the camera because that never changes and requires demosaicing into an image format before it will even look like an image. This article was helpful in understanding raw and dng files. Sorry if I ramble on but I've been trying to explain to myself what I and others are experiencing.
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