How to include text intended only for reviewers in main manuscript submission?
You mentioned the online e-companion approach which works well in some situations. 

Another I've used is adding an Appendix to the paper so it is organically included in the initial submission only. We explicitly label it for the reviewers' convenience only and that it will be removed from the final version. After the first round of reviews, we typically remove it and place as an appendix in our Response to Reviewers. This has been convenient for us as authors and for the editor. It may not work for all situations.