A possibility we have considered but the families concerned all lived in a fairly small area and would have been known to others in the locality. In any case there is little evidence of ordinary families being hounded for political reasons after the Civil War, and these families were tradespeople and agricultural workers, not gentry and certainly not connected to royalty !
Also note that the families often baptised their children under both names, which they would hardly have done if trying to escape the attention of the authorities.
The use of aliases during the period up to the mid-1700s was relatively common and seems to have been more to do with avoiding confusion between branches of the same family with the same Christian names living in the same locality. One branch would adopt an alias surname in addition to their original surname much as in later years people started using hyphenated surnames to distinguish different branches of the same family.
Maec
