1. Presumably there is some standard governing how tags are written, de-facto or otherwise. I am not that familiar with flac-tags though, thats why the heading is written as a question, not a statement.
2. Yes, in fact i had some problems with it. But the reason i began with the comparison is that its not that uncommon for media progrs to change audio-data when writing tags. Before i let loose programs on my files i try to do my best to keep such problems from occurring.
3. I now the comments are readable, but the comments seemed to be the same (except tool name and version), however winmerge seemed to indicate a change in the beginning of the file in addition to the things written in the tags, that change was indicated as "mumbo-jumbo" in winmerge, which might indicate there is also a change in binary data? The tags themselfs are readable in plain text.
4. I like to control myself what data is written and not written to the tags, I sure its useful for someone, for me its just unnecessary tags i would rather be without
6 I tested again with foobar, it does not seem to change the numbering of the track, MC changes it from 01 to 1 when wrting the tag, foobar does not.
The flac-encoder is the tool for encoding flac-files. The one you download from
http://flac.sourceforge.net/download.html