Zurich Airport - how much time to clear customs?

The standard answer to your question is not to book anything in advance since you have so many variables that you cannot control. Things always happen that you cannot controls. For years we always booked the train or the ongoing flight with about a five hour window. Over the years that worked great sometimes with a little longer wait than we liked. Then about five years ago the US flight never left the ground and we lost about four hundred dollars of on-going flight tickets. We thought we had insurance but forgot to read the fine print.

To answer your question, Zurich airport is pretty efficient and train station is on the lower level. I would allow a min of three to four hours. A hour is way too short. Ninety minutes might be OK but everything has to click including take off on time in the US.

Related question would be if you are willing to a) buy train tickets that allow you to take a
different train if you miss your original one (although if you are willing to do that you might
as well just wait as Frank suggests) b) is there any implication or penalty if you try to pick
up your rental car early (there is also always the chance they just don't have any cars
available at that moment, Sion may not be that big a rental car depot).

I.e., I would look into what options you might have if everything goes smoothly, but I would
not plan on it unless you are aware of any penalties and contingencies. For instance,
do you know how to call the rental car agency if you're late, and will they give away your
car if you are late past a certain point.

You don't say when your trip is, but the ongoing EES introduction only increases the uncertainty
of how long it takes to get out of the airport.

My pre-EES experience is you will have your luggage and be at the train station in under 1 hour. Will your plane land on time? Problems with EES? Who knows.

You have the choice of 3 departures every hour to Sion, and and takes about 2 3/4 hours to get there. The cost for a ticket is 109 CHF pp 2nd class, good anytime for the day. If this trip is far in advance, you should buy Saver Day Passes now.

For most people, customs is just a walk through.

However, immigration/passport control is a variable nobone can guess. Especially with EES. (Only important if entering Switzerland from outside Schengen.)

There is a difference between passport control and customs.

A Saver Day Pass will save you worrying about train tickets (and potentially save you money if your trip is far enough in the future). So a time for the rental car company will have to be your best guess, plus communication with them about what happens if you are either early or late.

We arrived at 8 AM in Zurich in April. Wait was about 60 minutes (we had carryon luggage so no wait there). Note: There were digital passport ID machines that only a few people were using. Most just queued up in the disneyesque lines. I asked an official if we could use those digital machines (there were about 10 of them), she said sure. We did that, and got in a much shorter line afterwards (there are arrows on the floor telling you where to go). So try to do that first. Also, the folks we were traveling with had wheelchair assistance, and checked luggage. They were escorted thru both lines much faster than us, and were actually waiting on us at the end.
Also, in my own experience, it is better to be early than late for car rentals. So make your car rental for later than you think, and just show up early and politely ask if you can pick up your car at this time. The worst they can say is no you must wait awhile.

Happy travels!