Looking at your screenshot, it’s clear that you’re using other express payment methods from other payment gateway plugins, such as PayPal, alongside Elementor page builder for your checkout page.
Let’s clarify something to ensure we’re on the same page – are you setting the small icon size only in WooPayments, or are you doing this for all other plugins as well?
Furthermore, I’ve done a bit more digging for you, and it appears that Stripe determines the size of the button directly. This is why it might takeing up the entire section area instead of adhering to the plugin’s settings.
In the meantime, I recommend that you create a bug report in our GitHub report. This way, our developer can look into it and give you more detailed insights.