The value of lset is in working with single elements of nested lists, and probably more efficient than lreplace for replacing single elements of a simple list:
% lset myList {a b c d}
a b c d
% lset myList "" {a b c d}
a b c d
% lset myList 1 r
a r c d
% puts $myList
a r c d
% lset myList 1 b
a b c d
% lreplace $myList 1 1 r
a r c d
% puts $myList
a b c d
% set myList [lreplace $myList 1 1 r]
a r c d
% puts $myList
a r c d
%%%%
% set myOtherList [list $myList {h i}]
{a r c d} {h i}
% lset myOtherList {0 1} b
{a b c d} {h i}So you can use lset as in lines 1 and 2 with an empty index to set the initial list.
