Why does the original code behave differently when i use the while(<FILEHANDLE>) loop as a file handle to read a particular section of code(say between line 2-10) instead of using EOF ..???

Because while( <DATA> ) { reads and discards a line each time it is executed. And that line contains a header (or data) that is required.

If you need to skip 29 lines, do so before entering the while loop:

<DATA> for 1 .. 29;
until( eof( DATA ) ) {
...
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And to exit the loop after the 40th line has be read:

until( eof( DATA ) ) {
    last if $. == 40;
    ...
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