In computer science, if you say "A is a proxy for B", then it means that "A replaces B" (temporarily or not), or that "A is used as an intermediary for B".
The term "proxy" usually refers to a server, i.e. there are the so-called proxy servers, which intuitively do the same thing (i.e. they are used as intermediaries). The following picture is worth more than 1000 words.
Let's go back to your context. In the following paragraph
To develop DL techniques for synthesizing high-resolution realistic fundus images serving as proxy data sets for use by retinal specialists and DL machines.
The deep learning techniques will be used to generate data that will be used as a replacement for real data for use by retinal specialists.
In your second paragraph
The advantage of the product state-based view is the focus on the product itself to structure the information and data involved throughout the process. Using the intermediate product states as proxy data for this purpose
The word "intermediate" is even used, so there should not be any need for further explanation, although I admit that I have no idea of what "product states" are in this context, but they will be used as "proxy data" for other data.
Does "proxy data" mean the same thing as "proxy data sets" does, if yes, I will go through that paper.
I guess so, but bear in mind that "data" is more general than "data set".
I have found other slightly different uses of the expression "proxy data", not in the context of computer science, but in the context of paleoclimatology. For example, have a look at this web article What Are Proxy Data?.
Just for completeness, here are some dictionary definitions of proxy.
authority given to a person to act for someone else, such as by voting for them in an election
a person who you choose to do something officially for you
a situation, process, or activity to which another situation, etc. is compared