I think you are right.
Neither Malcolm nor Alexander Left Scotland.
I think you can safely assume that Duncan and Malcom are not the same person!
:
Alexander McGilivray and Georgina Lindsay married in Perthshire 1882
1891:
Ashentean House, Glenorchy, and Inishal, Argyll
Alexander McGilvera 31 b Argyll. Occ Shepherd
Georgina McGilvera 28 b Crieff, Perthshire
Isabella McGilvera 8 dau b Fife
Christena McGilvera 6 dau b Glenorchy
Grace McGilvera 4 dau born Glenorchy
Georgina McGilvera 2 dau Born Glenorchy
Hugh McGilvera 1 son b Glenorchy
(Ist son and 2nd daughter are traditionally named for thr father's parents, and above looks about right)
1901: Cadderley Farm, Muckairn, Archattan and Muckairn, Argyll
Alexander McGilvray 41 b Mull. Shepherd
Georgina McGilvray 32 wife b Crieff
Georgina McGilvray 12
Hugh McGilvray 10
Duncan McGilvray 9 son b Glenorchy
Alexander McGilvray 6 sonb Perthshire
James Burns McGilvray 4 son b Perthshire
Sarah McGilvray 3 daughter b Ardchattan
Charles McGilvray 1 son b Ardchattan
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AND Malcolm :
looks like he married Isabella McDonald in Mull 1881
1891:
BURG Kilfinichen ( Parents former home)
Malcolm McGiloray 37 b Torosay. Occ Shepherd
Isabella McGiloray 30 Wife b Kilfinichen
Hugh McGiloray 9 son b Torosay
Neil McGiloray 7 son b Torosay
Duncan McGiloray 3 son b Torosay
Alexr McGiloray 1 son B Torosay
1901 Same address as 1891
Malcolm Mcgilvray 57
Bella Mcgilvray 59
Neil Mcgilvray 17
Duncan Mcgilvray 12
Sandy Mcgilvray 11
Coll Mcgilvray 9 son B Kilfinichen
Duncan Mcgilvray 7 son b Kilfinichen

??
Christy Mcgilvray 3 dau b Kilfinichen