Slightly revised version of submitted paper two days afterwards: will the editor be annoyed?
The more you wait the harder it gets to do that, there could be a pipeline that is already in progress. I suggest you send a nice email asking if there is a possibility to do this, and show that you would appreciate if he/she accepts the slightly updated attached version as the final version. 

Do not worry about making the editor mad, he/she took responsibility for taking care of this and should be prepared for and expect to deal with such situations. If you want to maintain a good relationship with this editor (in case you know him/her personally), then maybe you should weight the values of: your relationship with the editor vs the quality of the final version. Personally I would go for the latter, but this is your call.