Firstly, note that your transform-matrix function contains exactly one instance of the '(t 0) syntax, whereas the expression you're testing at the REPL contains two instances: (eq '(t 0) '(t 0)).
Because that expression has two instances, it is is possible that those will be different objects. In fact, the Lisp implementation would have to go out of its way to turn them into one object, and it is something that is allowed.
The (t 0) syntax is a piece of the program's source code. A program can apply the quote operator (for which the ' character is a shorthand) to a piece of its syntax to use that syntax as a literal. A given literal is one object; multiple evaluations of the same quote yield the same object.
When Lisp is naively interpreted, the interpreter recursively walks the original list-based source code. The implementation of the quote operator simply returns the piece of code that is being walked as a value.
When Lisp is compiled, the list-based source code is transformed to something else, such as native machine language for the CPU to execute directly. In the transformed image, the source code is gone. Yet, the compiler has to recognize the quote special form and translate it somehow. To do that, it has to take the piece of source code structure enclosed by quote and embed that object in the compiled image, so that it's somehow available to the compiled code: i.e. that quoted part of the source is not gone, but is propagated into the translation. For instance, the compiled image may be accompanied by a static vector dedicated for storing literals. Whenever the compiler process a quote expression like '(t 0), it allocates the next available slot in that vector, like position 47 or whatever, and stick the object (t 0) into that slot. The compiled version of '(t 0) code will then access that slot 47 in the literal data vector, and it will do that every time it is executed, retrieving the same object each time, just like the interpreted version of the program retrieveds the same piece of its own source code each time.
When compiling literals, the compiler may also search through the vector and de-duplicate it. Instead of allocating the next available index, like 47, it might scan through the literals and discover that index 13 already has a (t 0). Then it generates code to access index 13. Therefore, the compiled version of (eq '(t 0) '(t 0)) may well yield true.
Now, the way your question is framed, there is no evidence that there is an actual problem from all of the slots sharing a single instance of (t 0).
You need these objects to be different if you ever change the 0 value to something else by mutation. However, even that issue can be solved without actually making the objects different up-front. So that is to say, we can keep all the (t 0) entries objects pointing to the same object, and if we want to change some of them to, say, (t 3), we can allocate a whole new object at that time, rather that doing (set (cadr entry) 3). Moreover, maybe we can make all the (t 3) entries point to a single (t 3), like we did with (t 0).
It is impossible to say that changing '(t 0) to (list t 0) is the best approach to fix the problem, assuming there even is a problem.
(mapcon #'(lambda (x) '(1 2 3)) '(1 2)). looks harmless, right? - Will Ness