Multi Step Merge

You could also try unpivoting both tables before merging.

I don't know if this will be any faster but you can try something like this:

let
    Source = Table.FromRows(Json.Document(Binary.Decompress(Binary.FromText("i45WSjRU0lFSyMvPK04FIgU4QBZVitWJVoJzdJScjHDKYtEN4iQbo5uhgJUNUgRUi08aSSIZtzvQjHA2RJdNMoQ6KxYA", BinaryEncoding.Base64), Compression.Deflate)), let _t = ((type nullable text) meta [Serialized.Text = true]) in type table [A = _t, B = _t, C = _t]),
    #"Changed Type" = Table.TransformColumnTypes(Source,{{"A", type text}, {"B", type text}, {"C", type text}}),
    #"Added Index" = Table.AddIndexColumn(#"Changed Type", "Index", 0, 1, Int64.Type),
    #"Unpivoted Columns" = Table.UnpivotOtherColumns(#"Added Index", {"Index"}, "Column", "Value"),
    #"Uppercased Text" = Table.TransformColumns(#"Unpivoted Columns",{{"Value", Text.Upper, type text}}),
    #"Merged Queries" = Table.NestedJoin(#"Uppercased Text", {"Column", "Value"}, Table1, {"Column", "Value"}, "Table", JoinKind.LeftOuter),
    #"Expanded Table" = Table.ExpandTableColumn(#"Merged Queries", "Table", {"Ref"}, {"Ref"}),
    #"Filtered Rows" = Table.SelectRows(#"Expanded Table", each ([Ref] <> null)),
    #"Grouped Rows" = Table.Group(#"Filtered Rows", {"Index"}, {{"Ref", each List.First([Ref]), type text}}),
    #"Merged Queries1" = Table.NestedJoin(#"Added Index", {"Index"}, #"Grouped Rows", {"Index"}, "Grouped Rows", JoinKind.LeftOuter),
    #"Expanded Grouped Rows" = Table.ExpandTableColumn(#"Merged Queries1", "Grouped Rows", {"Ref"}, {"Ref"}),
    #"Removed Columns" = Table.RemoveColumns(#"Expanded Grouped Rows",{"Index"})
in
    #"Removed Columns"