Some questions of Calibre Conversion

[The_book]

After using Calibre Conversion, I have some questions.
First, why conversion between epub and azw3 or other html/xhtml format files causes change in class in files? It make editing them ugly.
Second, I perfer to store ebooks in markdown type, which is easy for me to search content from softwares like everything, and easy to compare to other versions of my file. And I know that I can use ebook-convert.exe filename.filetype .txt --txt-output-formatting=markdown to convert files. But is there any way to auto rename the output .txt file as .md or use ebook-convert.exe filename.filetype .md to convert files.?
Third, after some test on chm and searching on this forum, I believe Calibre convert .chm file in the logic that the first page is toc page and the rest is just content. But why it still do this when the chm file having toc file .hhc in it? I think just follow the toc file is better for always regard the first page as a toc page