If you change your data to:

typedef struct {
    float one;
    float two;
    int   three;
    bool  potato;
} struct_name;

typedef struct {
    float one; /* 1.1 */
    float two; /* 2.2 */
    int   three; /* 3 */
    bool  potato; /* true */
} struct_name_with_comments;
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You get the following (wrapped to compress):

$VAR1 = 'struct_name_with_comments';
$VAR2 = [
          ['float', 'one', 0],
          ['/*', '1.1', undef],
          ['/*', '2.2', undef],
          ['/*', '3', undef],
          ['/*', 'true', undef]
        ];
$VAR3 = 'struct_name';
$VAR4 = [
          ['float','one',0],
          ['float', 'two', 0],
          ['int', 'three', 3],
          ['bool', 'potato', 'false']
        ];
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There appear to be bugs :).

Given you are $line =~ s/\n/ /g; and $line =~ s/\s+/ /g; you could just $line =~ s/[\n\s]+/ /g;.

<>.The use of $/ is nice. Good to see someone remembering it's there.