I can't answer how Z3 works. I can only speculate on some possible ways one could build a solver for this type of constraints, if one wanted.
It appears all of your inequalities have the form
$$A \le \min(B,C) - \min(D,E)$$
where $A,B,C,D,E$ are linear expressions of the variables, i.e., each has the form $a_1x_1 + \dots + a_nx_n + b$, for some constants $a_1,\dots,a_n,b$. This is equivalent to
$$\min(F,G) \le \min(H,I)$$
(take $F=D+A$, $G=E+A$, $H=B+A$, $I=C+A$). This is equivalent to the two inequalities
$$\min(F,G) \le H, \min(F,G) \le I,$$
which in turn is equivalent to the two inequalities
$$\min(F-H,G-H) \le 0, \min(F-I,G-I) \le 0.$$
So, without loss of generality, we can assume you have a system of inequalities of the form
$$\min(U,V) \le 0$$
where each $U,V$ are linear expressions of the variables (with different constants).
I don't know how Z3 solves such a system of inequalities, but one approach is to use integer linear programming (ILP). In particular, for each such inequality, we can introduce a new variable $t$, constrain $t$ to be an integer, and add the following inequalities:
$$\begin{align*}
t(U) + (1-t)V &\le 0\\
V &\le U + tM\\
U &\le V + (1-t)M\\
0 &\le t \le 1
\end{align*}$$
where $M$ is a large constant (larger than the largest possible value of $|U-V|$). This is a big-M method, as you mention in your question, and as you indicate in the question, it's not guaranteed to work correctly if we don't have an upper bound on the value of $|U-V|$.
I don't know whether Z3 uses this technique, or if it does, how it deals with the lack of any known upper bound on $|U-V|$. One possible heuristic would be to guess at a large value of $M$; try to solve the corresponding ILP instance. If there is no feasible solution, then we know there is no feasible solution to the original problem. If there a feasible solution to the ILP instance, we can check whether it solves the original problem. If it solves the original problem, we can output it. If it doesn't, we can double $M$ and try again. I don't know whether there are any guarantees that this will ever terminate, but it is a possible heuristic.
Another possibility is that Z3 might internally use a SMT solver, specifically, SMT with linear inequalities over real variables. It is easy to express your problem as an instance of such a SMT formula, and there are sophisticated SMT solvers for testing satisfiability of such formulas. I suspect this might be the most likely possibility, but I don't have a basis for this suspicion.