At page 776 of House of Commons Procedure and Practice on the report to the House, it says:
The committee is bound by its order of reference—the bill—and may report the bill only with or without amendment to the House. Consequently, the committee may not include substantive recommendations in its report.
And further down the paragraph:
However, there is nothing to prevent a standing committee, under its permanent mandate in the Standing Orders, from presenting a separate report in which it sets out substantive recommendations with respect to the subject matter of the bill.
The chair would report the bill to the House as adopted today with the amendments. Basically, the report would contain all the amendments that were adopted today, and when you table the report, you could also say that there are other recommendations that may come down later on in a separate report from the committee.