is the French certificate of renewal of CNI enough to prove my identity in Switzerland

Note that France extended the validity of some French national ID cards from 10 to 15 years:

https://www.interieur.gouv.fr/Actualites/L-actu-du-Ministere/Duree-de-validite-de-la-CNI (mirror) contains a list of countries that are supposed to accept or reject such expired French ID cards. Switzerland is in that list. It also contains some text explaining the five-year extension translated in the language of each country, which you want to keep a copy of when traveling. Lastly, it advises:

De façon à éviter tout désagrément pendant votre voyage, il vous est fortement recommandé de privilégier l’utilisation d’un passeport valide à une CNI portant une date de fin de validité dépassée, même si elle est considérée par les autorités françaises comme étant toujours en cours de validité.

Google Translate:

In order to avoid any inconvenience during your trip, you are strongly recommended to privilege the use of a valid passport to a CNI carrying an expired date of validity, even if it is considered by the French authorities as being always in validity.

The EU free movement directive calls for beneficiaries who lack the required documents to be given an opportunity to prove by other means that they are covered by the directive. In other words, if you can prove that you're French, you should be allowed to enter.

This directive does not apply to Switzerland; instead, there is a bilateral agreement between Switzerland and tbe EU that provides for broadly similar rights. I don't know whether the same provision is in that agreement, but I suspect that it is, because the Swiss government has this to say on their frequently asked questions page:

3.1 May EU or EFTA citizens without a valid travel document or without a travel document made out in their name enter Switzerland?

In principle, anyone who wishes to enter Switzerland is required to hold a valid travel document in their name (a passport, emergency passport, temporary passport, ID card, or a special travel document issued to children). Depending on nationality, certain expired travel documents are accepted by Switzerland for crossing the Swiss border:

List: Overview of ID and visa provisions according to nationality.

EU or EFTA citizens wishing to enter Switzerland without a valid travel document will be admitted if they manage to prove or make credible their citizenship. The burden of proof lies with the person concerned and in case of children with their parents or accompanying adults. Proof of citizenship may be furnished by any appropriate means. The State Secretariat for Migration (SEM) suggests carrying the following documents:

• a photocopy of a valid travel document;
• an expired travel document;
• an official document proving the identity and/or citizenship of the holder (e.g. driver’s licence);
• for children: an extract from an official register (e.g. the register of births, marriages, and deaths) and/or the original of the child's birth certificate if no such official register exists or if no extract could be issued for lack of time.

In all cases it is strongly recommended to apply for a travel document as soon as possible.

Please note that certain airline companies may not transport passengers without valid travel documents. Please check with your airline what transport conditions apply.

I have crossed the border between France and Geneva several times in the last year, by train, bus, tram, and auto, and I've never been stopped or questioned by any government authorities except in the car. Those inquiries were all limited to customs concerns. There was never any question related to nationality or immigration/residence status (despite my asking in every case for the officer to conduct the interview in English).

Passengers for trains from Geneva to the west (and vice versa), that is, not via Annemasse, have to pass through a customs checkpoint in the Geneva train station. I've never been stopped by the officers there, but I expect that the inquiry would be limited to customs questions as with the road crossings I've experienced.

If I were you, I would not modify my plans on account of the expired ID card. Bring the renewal certificate and whatever other documents or copies might help to establish your identity and citizenship. You'll almost certainly not need them, but if you do, they'll almost certainly suffice.