I have tried that exact setup for creating the Subscription Plan Variation and Payment Link (using PHP SDK) and it has yet to work. It will only show the one fee, it does not show the two different fees in the Checkout UI. I don’t know if I am setting it up right and that is just how the UI looks or if I am doing something wrong.
That is correct and the expected behavior with the Square provided UI. It will
NOT display the second phase. 
So if I have $150 up front and $100 per year, the UI is still wildly wrong.
Example: CleanShot 2025-01-15 at 11.12.06 · CleanShot Cloud
It says $150/year when that is not the case - it is $150 now and $100/year thereafter.
I got this Payment Link using the Explorer to ensure it is all working correctly.
After the customer pays they will get an email conformation. In that email it will have the second phase. Ideally leading up to the payment link being created your flow should disclose the various phases of the subscription. Then the button can say something like “Start the subscriptions with a $150 payment.” That way they’re not confused and when they see the amount $150 in the UI. Nor are they surprised by the $100 amount in the conformation for the second phase.
I can put all those things in place but the fact that the Checkout UI says $150/year and “Ends Jan 2026” is both completely wrong and wildly confusing to users, regardless of what shows before/after or in an email. It’s simply inaccurate and not good UX whatsoever.
We’re constantly working to improve our features based on feedback like this, so I’ll be sure to share your request to the API product team.
Would there be any way to show just the initial flat price? Our team said we can work with that and not show the annual recurring since we do show that before/after the Checkout page, but the deal breaking issue is the “$150/year” and “ends on” parts.
Could it be done via line items instead maybe?