maxSynapsesPerSegment is just the max, it will only query the synapses that have actually formed. That said, if cells learned many connections then it could get slow (and cell predictions could have many false positives)
Getting rid of separate segments (#2) is a reasonable idea and the algorithm should still work, although I wouldn’t set the max synapses that high. There is some ability to handle unions without confusion - i.e. if there are three sets of presynaptic cells that put a post-synaptic cell into a predictive state, it is unlikely that the cell will have a false positive (going into predictive state when none of the three patterns are active but some small subset from each are active). Once you get up to 10, 15 patterns unioned together you will start to see false positives. You can manage this somewhat with the right learning rates and limiting maxSynapsesPerSegment but it is much easier when you have multiple segments.