Hi, I am no deep-dive-developer, but I understand the root of your question, so here it goes:
You are trying to approach this point from a gaming point of view, where pushing more pixels means slowdown. In the case of gaming, the bigger screen will result in 50% (lets just pretend that pixel count makes a linear increase in power needs) more strain to GPU.
On the other hand, Affinity Photo computes the pixels that are on canvas, as well as effects on those pixels. Say, a 1280x800 (a 1 megapixel image that we use here for reference) will eat up exact same resources on both iPads (the image will also fit on both screens perfectly, thats why I chose this resolution). Applying CPU intensive live filters (perspective wrap + gaussian blur at the same time) will make the exact same load on both iPads, regardless of their resolution, since all they have to do is to live-calculate 1 megapixel in real time.
Answering your question, I would suggest you go with the 13" one – you will squeeze more productivity out of the bigger screen.
PS - I myself run on 9,7" iPP and plan on upgrading this summer to newer ones. 120Hz and overall increase in power will be mind-blowing.