The model has to be written to use the non-TR-locked times. If you're writing your own C model, the model can use the x_array structure where time is handled as xarray[timeindex][1]. You can see lots of examples in the existing C model files in the AFNI source code. There is some more descriptive info in Doug Ward's documentation for 3dNLfim.
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afni.nimh.nih.gov]