Primary key addition for a table which contatins no data is too slow
You are running in Windows, correct?  Perhaps an older version of Windows and an older version of MySQL?  File operations are slow.  ALTER TABLE, especially when changing the PRIMARY KEY, requires creating 1-3 files, copying over some stuff (not much in your case), removing the old 1-3 files, then renaming the files.

ALTER on an empty table is not a priority.  However, some improvements were made in 5.6 on Windows.  Still, I suggest that Windows file management is the main culprit. Your code may have added up to 27 system calls for file manipulation.  15 seconds seems about right for Windows.

You could speed the process up by combining the statements:

ALTER TABLE Table1
    DROP PRIMARY KEY,
    ADD Column3 INT(10) DEFAULT '1',    -- (I fixed the syntax error here)
    ADD PRIMARY KEY Table_PK(Column1, Column2 , Column3 );


With few exceptions, you can combine multiple ALTERs for a single table into a single ALTER.  And, unless all can be run with ALGORITHM=INPLACE, it is faster to combine them.

Consider using INT UNSIGNED for Column3.  And/or some smaller type of INT, such as SMALLINT.