The highlighted use of "in" in your sentence is part of a two-word term "in which". That term is then referring to the "relationship" (or, arguably, the "interaction", but those words are interchangeable for this example).
This sentence...
A symbiotic relationship is an interaction between two or more species in which one species lives in or on another species.
...comprises two concepts, both of which regard "A symbiotic relationship", and joins them with the "in which" term. Personally, I find that the structure could benefit from the addition of a comma after "species", for pacing and clarity, so:
A symbiotic relationship is an interaction between two or more species, in which one species lives in or on another species.
From here the two-concept sentence can be broken-down into...
1.) A symbiotic relationship is an interaction between two or more species.
2.) In a symbiotic relationship, one species lives in or on another species.
Or, more heavily...
2.) A symbiotic relationship is a relationship in which one species lives in or on another species.
Of those last examples for the only second concept, the first example is cleaner and less redundantly worded, and an editor may suggest changing a sentence built like the second example to read like the first version instead. They mean exactly the same thing.
Joining them together, the use of "in which" is a sort of "call-back" to an earlier part of the sentence, so that you can further condense on the page the information you wish to convey, without losing detail. Without the first section describing the relationship, this break-away sentence...
One species lives in or on another species.
...might be complete as far as it goes, but it leaves questions unanswered about what our over-all subject is. Merely including it as a second sentence after...
A symbiotic relationship is an interaction between two or more species.
...leaves a very awkward construct:
A symbiotic relationship is an interaction between two or more species. One species lives in or on another species.
While a reader can make sense of that, they have to pause to think about it, just a tad. That structure dissociates the concepts slightly, when the purpose is to make sure they go together. Another expanded way to build the sentence would be:
A symbiotic relationship is an interaction between two or more species; [a relationship in which] one species lives in or on another species.
Note that the [bracketed] portion is what goes together, and would be said in one breath if it was being read aloud. There's a risk for a learner to see "which" and "one" next to each other, and take it as the question phrase "which one?", and that would certainly make a mess of things. Having the word "in" in that location makes a lot of difference, and is fused with "which" to make it all work.
Once more:
A symbiotic relationship is an interaction between two or more species in which one species lives in or on another species.
(And I still think that's missing the comma, but that wasn't the question.)
Reference: I'm a native speaker of American English, born and raised in California, with some college, and a parent who is a published author. But to be frank, the use of "in which" is a bit stuffy, and I associate such a construct with more-formal British English. It still works in America just fine, though.
Best Answer
Their refers to "facilities for self-service", since it's those facilities that "provide goods of every description attractively and hygienically and in perfect condition".
Although the shops, stores and supermarkets also provide this, the Law of Proximity would lead one to attribute it to self-service facilities.