Swiss Transfer Ticket

No, the Swiss Transfer Ticket can only be used along the most direct route to your destination and does not allow a detour to Zermatt in one day and especially not via the Glacier Express (unless it's the fastest, most direct route from your border entry to an end point at Zermatt). It may be hard for them to administer misuse on some routes, but on this one would be pretty easy to spot. Maybe you were planning to count it as two travel days, but that still sounds risky. If you don't need any further travel, you would probably just buy those two tickets. Or, a Swiss Travel Pass for 3 consecutive days costs $224 per person or a Half-Fare Card costs $128 per person (then you pay half of your estimated ticket costs).

Jenny, you wrote "Tickets aren't available for purchase yet". Switzerland is one of the few countries where the price is always the same. There is no price advantage for buying tickets early, no advanced booking (no reserved seats), and all tickets are valid on any train.
Just buy your tickets on the day and get on the next train.

Zürich HB to Zermatt: 3h11 = CHF 123 (this is cheaper than a Swiss Transfer ticket at CHF 141)
Zermatt to Genève: 3h45 = CHF 96
(123 + 96) * 2 = CHF 438

But, this does not include the Gornergratbahn at CHF 86 per person return (click here for prices) or the time needed (click here for timetable). This will be a long and expensive day.

You don't have anything budgeted for the Gornergratbahn, which is pricey as well. That is 86 chf per person round trip to the top. So that makes two 120 chf Half Fare Cards pay off.
If this is a one day trip, you have no guarantee that the weather will cooperate and give you a view of the Matterhorn no matter what the view point is.

Here is another option. See if you can get Supersaver Tickets. They are only available on-line 2 weeks out. I just looked at April 17, and you can get 2 tickets Zurich to Zermatt in the morning for 166.40 chf total, and 2 tickets Zermatt to Geneva for 96 chf total in the late afternoon. Two separate transactions. That's 262.40 total which is a bit less than 438 chf. You're still on the hook for full price on the Gornergratbahn.
http://www.sbb.ch/en/travelcards-and-tickets/tickets-for-switzerland/supersaver-tickets.html

Thanks all, I am a chronic planner and love buying in advance. I will resist my planner's nature and wait until we get to Switzerland to buy those tickets as you are right, there is no advantage to early purchase. I did not list Gornergrat as it would not be covered by the Swiss Transfer or even Swiss Rail, I believe. I was just focusing on the main tickets. It sounds as though I am just going to have to suck it up and figure on paying full price. Yes, it will be a long and expensive day, just hoped I could cut the cost by some.