The answer is quite simple, what is meant by the symbol $t$ in the case of the Friedmann metrics is always the comoving time.
This is generally the case when presenting a metric, the coordinate statements of course relate only to that given coordinate system. Consider the Schwarzschild space-time. There we have Schwarzschild coordinates $r,t,\varphi,\vartheta$. The fact that the space-time is static, all the metric components are independent of $t$, is true only in the given coordinate system. In particular, the "$t$" in the Schwarzschild coordinates is proportional to a time measured by a very special class of observers, the static observers, and these will thus see the space-time as static.
Naturally, the Schwarzschild black hole will seem non-static to any other observer class, the black hole will generally seem to be moving with respect to the non-static observers. This would be reflected in the metric coefficients being dependent on the new "non-static" time $\tilde{t}$ if a corresponding coordinate system was to be adapted.
This is very much the case with the FLRW space-times (please keep the Lemaître if you include the Robertson and Walker). The statements about the metric coefficients being dependent or independent on coordinates are of course true only in the given coordinate system. In this case the time would be only the time of the comoving observers and the spatial directions the orthogonal directions to that.