The context for understanding the thermodynamics of quark matter is the standard model of particle physics, which contains six different flavors of quarks, as well as leptons like electrons and neutrinos.  These interact via the strong interaction, electromagnetism, and also the weak interaction which allows one flavor of quark to turn into another. Electromagnetic interactions occur between particles that carry electrical charge; strong interactions occur between particles that carry color charge.
The correct thermodynamic treatment of quark matter depends on the physical context. For large quantities that exist for long periods of time (the "thermodynamic limit"), we must take into account the fact that the only conserved charges in the standard model are quark number (equivalent to baryon number), electric charge, the eight color charges, and lepton number. Each of these can have an associated chemical potential.  However, large volumes of matter must be electrically and color-neutral, which determines the electric and color charge chemical potentials. This leaves a three-dimensional phase space, parameterized by quark chemical potential, lepton chemical potential, and temperature.
In compact stars quark matter would occupy cubic kilometers and exist for millions of years, so the thermodynamic limit is appropriate. However, the neutrinos escape, violating lepton number, so the phase space for quark matter in compact stars only has two dimensions, temperature (T) and quark number chemical potential μ. A strangelet is not in the thermodynamic limit of large volume, so it is like an exotic nucleus: it may carry electric charge.
A heavy-ion collision is in neither the thermodynamic limit of large volumes nor long times. Putting aside questions of whether it is sufficiently equilibrated for thermodynamics to be applicable, there is certainly not enough time for weak interactions to occur, so flavor is conserved, and there are independent chemical potentials for all six quark flavors. The initial conditions (the impact parameter of the collision, the number of up and down quarks in the colliding nuclei, and the fact that they contain no quarks of other flavors) determine the chemical potentials. (Reference for this section:).