Well, it sounds like you expect MC to have some sort of specific export option for an itunes-native playlist. The correct approach when trying to transfer data between programs is to know (or research) what file formats (playlists, in this case) they have in common.
If you had done a google search for importing playlists in itunes, you would have learned itunes supports the M3U format. That is what you should use when exporting in MC.
The order of the playlist WILL be maintained.
I don't know how familiar you are with either software package, so if you import a playlist into itunes that way and believe the playlist order is not maintained, I have to wonder if you know what the playlist order actually is...
First, you're wasting your time looking for the seq number in explorer or in the tags. The seq number exists only in the context of the playlist, and in the playlist file or its structure. Also, the order the music files are displayed in explorer is absolutely irrelevant, as is the order in which you convert file formats, as is the order in which you add the music files to itunes. You are confused on that issue. Order, or Sequence, only exists with the playlist.
In MC the playlist has exactly one "official" order, the Seq order. This is the order in which the files are added to the playlist, period. It can be then manually changed by drag and drop, or by other means. You will know the Seq order of the playlist by looking at the Seq(uence) column. The Seq order is the order files will be in the M3U file, and the order itunes will have them in. If you want to see the true order of the playlist, sort by the seq column.
Now since I don't know how much you know, it may be that you might not realize in MC you can DISPLAY the playlist in any order you want, by clicking on the column headers. This will make it look like the playlist is in a certain order (like if you click on the name column, the list will be sorted alphabetically by name) but this does NOT actually change the order of the playlist. Look at the seq numbers when you sort the playlist different ways: they don't change.
In this way, someone could think itunes is not respecting the playlist order, because the itunes order does not match how things are displayed in MC. But in fact, they are simply displaying the playlist OUT OF ORDER in MC. There is an right click option to update the seq to match the displayed order, and there are other ways to change the seq order. Google jriver playlists to learn more.
Getting the music files themselves into an iPod compatible format is a different matter. It seems you have figured that part out.
If you export the playlists in M3U format, and use the "File->Library->Import Playlist" option in Itunes, the order will be maintained. Just make sure you truly have them in the correct playlist order first, and that the files referenced in the M3U exist in the Itunes library. If the files specified in the M3U playlist do not already exist in the Itunes library, itunes will ignore them. If you don't have the itunes-format file in your MC library, then when you export the playlist, the playlist will reference the FLAC file, and Itunes will ignore it. You can do a search & replace on the M3U file to change the file extension and paths to what Itunes expects.
(I will mention that on the MC file menu there is an option "Export to Itunes" that is a one-stop solution for this, but it requires you to have the Itunes-compatible files (MP3, ALAC, etc) in your MC library. Itunes does not support FLAC, and if you use this function to export FLAC files or a playlist that contains FLAC files, Itunes quietly ignores them, so you get nothing.)
So if the goal is to import into itunes an MC playlist where the files are FLAC (a format Itunes does not support), and you refuse to keep the itunes-compatible files in your library, you basically have to do this:
1. Convert the files to MP3 (or whatever)
2. Put the MP3 files somewhere, and import them into itunes
3. Export the playlist as M3U
4. Edit the M3U playlist using Search & replace to change the .flac extension to .mp3, and fixing the path to the files to match the path to the mp3 files. This takes seconds.
5. Import the edited playlist into itunes.
You're finding a lot of faults with MC in this situation, and it is certainly not a perfect program, but the reality is you wouldn't be having any of these issues if Itunes supported FLAC. MC will work with pretty much anything. Apple dictates you use their preferred formats.
I hope this helps.
Good luck...