Hello:
There is a related discussion here: How can i get time-series plv
Brainstorm lets you estimate time-resolved PLV across trials or blocks, if this is relevant to your experimental design (i.e. phase consistency across blocks). There is no windowing in the PLV calculation as the phase is extracted using the Hilbert transform on band-pass filtered data. Hence there is no spectral decomposition involve that would require windowing.
Hope this helps.