Are these three batteries of the same type, or only with the "same chemistry"? In general, 3 samples are the minimum number of set for any conclusions about the characteristics. In fact, you split this set into three (different charging methods), so each is based on a single sample, therefore you can not draw any meaningful conclusions, taking into account that batteries are already initially different (production can not give absolutely equivalent batteries).
Initial capacities should be same..., if these samples belong to the same batch (in error limits, of course). You discuss not capacity, but EIS. If you claim that the changes are related only to the battery charge method, every normal person will ask you: "Are you sure that these samples had similar EIC characteristics before the experiment? Did you check this?" Moreother, near the fully charged (as well as the fully discharged) state, the internal resistance varies very much. Therefore, the change can be explained by varying charge degree (99.5 and 99.9% charge (not nominal, but real), for example will give very different picture). The charge current should also reflected. Measure the same spectrum after 2-3 days of relaxation and you will see a different picture. Conclusion: the experiment must be planned.
If you could remake the EIS measurements, using 4 cables[1], they will have quite the same (Nyquist plots).
1. see Fig.5, in: Advanced EIS Techniques for Performance Evaluation of Li-ion Cells http://folk.ntnu.no/skoge/prost/proceedings/ifac2014/media/files/2463.pdf