For example, the overall throughput is different. So, if you were worried about recombination and/or some amount of sample mixing (emphasizing the value of focusing on the most abundant sequences), maybe that could be indirectly relevant. Or, if you are purchasing your own sequencer, I would guess an iSeq/MiniSeq/MiSeq is more likely than a NextSeq (although some labs can even have their own HiSeqs).
From our experience it is better to compare samples sequenced using the same platform. Nevertheless, you can try to use your data derived from both MiSeq and NextSeq. It also depends on the data type, like if your data has UMIs (and new MiXCR version has a UMI support) you can use it to normalize data for more valid comparison.