There are two questions here:

1. Can eppy retain the original order of the idf objects in the file ? Answer: No

2. Can eppy retain all the original comments (starting with '!') ? Answer: No

Can you open separate issues for 1. and 2. at https://github.com/santoshphilip/eppy/issues/new. Describe the issues and propose a solution

Issue 1. may be easy to do. Issue 2. may not be easy to implement in eppy

If this can be implemented, this answer will be updated to reflect the functionality (If you don't open the issues, nothing will be happen :-)