I almost always make them self-contained. Technically there were just 3 exceptions during my whole career where I needed to "borrow" some big chunk of an established theory well-written in some easily accessible textbook that would be hard to compress into a short sequence of relevant lemmas needed for getting the result I need.
In my opinion, the purpose of writing a mathematical paper is acquainting the reader with either new result or a new (at least, for him/her) idea (the latter IMHO is more valuable, but much more rare as well) in the most efficient and the least painstaking way. Everything that goes towards this purpose should be welcome and everything that goes against it should be frowned upon.
Creating a long chain (if it were just a chain, usually it is a branching tree growing exponentially in size when you try to dig deeper and deeper!) of references, IMHO, impedes the process of reading and makes the verification of the proof extremely complicated. You are no longer saying: "Here is the result and here is how to obtain it in the shortest way from the basic principles", thus putting it in the context of not the irrelevant temporal history of who did what and when or what is the latest fleeting fad of the times, but in that of what exactly was really needed to be developed before your approach/technique/observation became possible as it is. Instead you downgrade your exposition to the conditional statement that "if 5 references I give, 25 references contained in those 5, 125 references contained in those 25, etc., are all correct, then what I'm writing follows" and create the (most often false) impression that to understand your work entirely, one needs to read several thick textbooks, several hard to get research papers often written in not the clearest possible way and proving only something similar to what you really need in a completely different notation and with a completely different emphasis, so you still need to make the final adjustment yourself. A 30-40 page argument written in a clear and coherent style becomes a monster encompassing thousands of pages of patchwork of loosely hanging fragments pulling in various directions and making the reader totally confused about what the main thing in the whole business is (note that the main thing in the proof is not necessarily the last step you added to it, even if the latter is truly novel).
That is about references the theorems. For just the equations, you can do it if all equations you need are contained in one textbook that is both well-written and easy to access and derives them sufficiently early in the exposition (so you don't need to read 300 pages of the linear text or do the painstaking backward search trying to figure out what on those 300 pages is relevant to what you are after to arrive at the result). If your advisor can come up with such a textbook, cite it. If he cannot, I would recommend denying his request for the appendix cut and keep the things as they are.
Now about My supervisor went on to say that others might think I am trying to steal their future citations by attempting to have people cite my paper for a formula that someone else came up with. Are you really "trying to steal"? If you aren't, don't bother too much about what other people might think (or even do think) about you. I'll tell you one unflattering truth: most of them do not think about you at all and are completely unaware of your existence and totally indifferent to it. When they are reading your work, they are interested in what is written there, not in you personally. Their goal is to understand your writing, not to judge your moral character based on it.
As to In my particular case, I am submitting to a journal with no page limits, albeit there are page charges that my supervisor will pay for., I believe that it explains the whole thing in a crystal clear way: your supervisor wants to spare a few bucks and, since people are usually reluctant to say such things plainly, invents a whole bunch of bogus "ethical" and other explanations of why the cut should be made. I have no idea about what moved you to the submission to a predatory journal in the first place (every journal that charges authors for their own work is predatory in my classification) while there are plenty of decent ones around (that is on the topic of "advice that I should carry with me throughout my career"), but once you've made such choice, you created an obvious conflict of interest, which you are trying to deal with now. In general remember that you don't need to publish anything beyond the initial minimal amount of few papers to get a decent position and then occasional couple of papers for promotion and such. You know how to prove the results you proved. It is the outside world that doesn't, and if it tries to make you pay money for sharing the proofs with it and going through the long painstaking process of creating the clear exposition in the form of "publication fees", "conference registration fees" and other modern nonsense, you are always free to send it to the Hell and keep the results to yourself, just sharing them with a few friends and colleagues in the form of private communication.
Just my 2 cents, as usual.