I believe SHELXL reports R1 cut at 4 sigma F and also R1 on all data, which I've got to bet is the source of those two different values. However I've never used SHELXL for protein and don't know if the cutoff is redefined for protein data.
No, but the fact that phenix.model_vs_data comes closer to the lower values (without discarding any data) suggests that the higher values don't reflect the statistics with cutoffs applied. (As expected, model_vs_data reports slightly lower R-factors when the cutoffs are used.)