Saving existing files in their native formats

Question

It's really annoying that Numbers insists on saving in its own proprietary format. Is there a way around this and is there a chance that the default behavior would ever be changed?
I've just had my first experience with Numbers since it was pre-installed on my new machine. I was opening a xlsx file a colleage had emailed me. I imagine that for many (business) users who don't create spreadsheets, this is a typical first interaction - opening an existing spreadsheet that somebody else has created. Business users are almost always using Excel or maybe you're opening a CSV because it came from a reporting system.
After making a small tweak to an existing CSV or XLSX file, Numbers prompts you to save in a new format - thus creating another file - or you can delete the new version you made. This isn't very user friendly.
Here's a common case. You might download an address template from a website in XLS or CSV and then fill it in and re-upload it. Workflow is very difficult in Numbers and especially so for a novice user. It's not intuitive to have to go to the export menu to save it in the same format it was already in.
For some background, I run engineering at an ecommerce startup and I've used Excel, OpenOffice and Google Docs for years and typically stick to the latter two these days since they're free. We install OpenOffice on all our Macs to crunch bigger spreadsheets (vs Google Docs) and of course like that it's free.
I realize that the native format has its advantages and Apple also has reasons for wanting to convert to their own format, but in some cases where fidelity isn't affected, saving changes to an existing file just makes a lot more sense.

Answer 1

I was primarily looking for supported way to solve this use case but it sounds like that isn't available out of the box. In that case, no need to spend any more time looking into this. SG, your workaround is pretty admirable and that's a good idea, but it probably doesn't make sense usabillity wise when you could use a text editor if you were advanced enough as you mentioned or just use another program.
Wayne, as you suggested, I submitted feedback from Numbers itself so hopefully that helps the Apple team understand this use case better.
For internal use, it sounds like using another program is the most straight-forward way for this case (for average users). However, since we have a website with tons of Mac users, it's realistic that the default xls or csv handler on their system is Numbers so there won't be a way around that. Of course we can't tell users on our site to download a script to make saving a file any easier (since it would be harder), so I think the best thing is to give users instructions with the steps I outlined even though there are lot of them. It sounds like there's no better way for general users.
Thanks for all your help guys!