I have two instances where William Innes and Margaret McAlister appear. There is one where only Captain Innes and his lady Mrs Innes appears. The name that appear are as follows:
1) William Innes born 28 May 1771 ( Thurso ) ( in Town )William Innes and Margaret McAlister are parents.
2) William Innes born 20 Aug.1779 ( Thurso ) ( in Town ) William Innes and Margaret McAlister are parents.
3) Christian Innes born 12 May 1788 ( Uphall or Strathbrock ) Captain Innes and his lady Mrs Innes are shown as the parents.

In Town, above was put in the birth register and I take that to mean that this family was passing occured.
Are you researching these names? Would love to hear from you.
In my opinion they are from the same family and I am satisfied to say that the fathers' name in these instances was William Innes and Margaret McAlister.
It does appear that William Innes was a Captain, not in the Navy but rather in a Regiment of Foot. Do you know which Regiment he might have been In 1771 and 1779

William In Montreal