Looking up his biography, he presumably wrote the first while imprisoned for fighting in support of CHarles II, and the second would seem to have conveniently been published around the same time as he left for continental Europe.
In the case of the Commonwealth, the UK empire was going strong and the guy was a royalist, aka supporter. The message "end the illegal war in Ukrain" aka Putin's genocide, does not really share a lot of commonalities here. If the message were to stop the Commonwealth from colonising everywhere and killing people then perhaps there would be a similarity, but I don't see the connection in the statement made here.
So in 1653, a 'royalist' was against the 'Commonwealth', which was the anti-monarchist side.
Urquhart was imprisoned from 1651-1652 for fighting on behalf of Charles II, who was King of Scotland until his defeat in 1651, and trying to take the English throne. He didn't get the English throne until 1660.