Oracle writes whole file during database creation is it ok

The answer to your question can be found in the SQL Language Reference (excerpt follows).

Creating Basic Tablespaces: Examples

This statement creates a tablespace named tbs_01 with one data file:

CREATE TABLESPACE tbs_01 DATAFILE 'tbs_f2.dbf' SIZE 40M ONLINE;

It sound like you are new to Oracle databases. Oracle provides a wealth of documentation at http://docs.oracle.com/en/database. Specifically, I recommend reading their excellent introduction to the database called the Concepts Guide.

The short answer is No. Unfortunately the way to do this in Oracle does require the "big stack of boring queries". The articles you linked to are some of the best information available on the subject. The datafile does indeed become fragmented, so that even if free space exists below the highest segment, Oracle will not automatically consolidate it when a RESIZE is done.

To "defragment" the tablespace you need to move these segments to the start of the datafile rather than at the end. For tables this is an offline process meaning the table will be unavailable while the move is taking place. Indexes can be moved either offline or with Enterprise Edition they can be moved online. Since you have an outage window I recommend you follow these steps.

A. Shrink datafiles with free space beyond the high water mark. This can be done as follows (the query is similar to Frosty Z's procedure):

SELECT ceil( blocks*(a.BlockSize)/1024/1024) "Current Size",
   ceil( (nvl(hwm,1)*(a.BlockSize))/1024/1024 ) "Smallest Poss.",
   ceil( blocks*(a.BlockSize)/1024/1024) -
   ceil( (nvl(hwm,1)*(a.BlockSize))/1024/1024 ) "Savings",
   'alter database datafile '''|| file_name || ''' resize ' || 
      ceil((nvl(hwm,1)*(a.BlockSize))/1024/1024/100)*100  || 'm;' "Command"
FROM (SELECT a.*, p.value BlockSize FROM dba_data_files a 
JOIN v$parameter p ON p.Name='db_block_size') a
LEFT JOIN (SELECT file_id, max(block_id+blocks-1) hwm FROM dba_extents GROUP BY file_id ) b
ON a.file_id = b.file_id
WHERE ceil( blocks*(a.BlockSize)/1024/1024) - ceil( (nvl(hwm,1)*(a.BlockSize))/1024/1024 ) 
   > 100 /* Minimum MB it must shrink by to be considered. */
ORDER BY "Savings" Desc;

B. After shrinking things above the high water mark, find out what tablespaces would still benefit from having segments moved.

SELECT DISTINCT tablespace_name FROM
(      
    SELECT tablespace_name, block_id + blocks LastBlock,
       lead(block_id) OVER (PARTITION BY File_ID 
          ORDER BY tablespace_name, file_id, block_id) NextBlock
       FROM dba_free_space 
) WHERE LastBlock <> NextBlock AND NextBlock IS NOT NULL;

C. For each of these tablespaces determine which segments need to be moved. (Replace USERS with the name of your tablespace or join it with the previous query)

SELECT distinct de.segment_name
FROM dba_extents de
JOIN
(
   SELECT tablespace_name, file_id, MIN(block_id) LowestFreeBlock
   FROM dba_free_space
   WHERE tablespace_name = 'USERS'
  GROUP BY tablespace_name, file_id
) dfs ON dfs.tablespace_name = de.tablespace_name AND dfs.file_id = de.file_id
WHERE de.tablespace_name = 'USERS'
AND de.block_id > dfs.LowestFreeBlock;

D. Move each table and rebuild the indexes and statistics.

E. Repeat step A.

I just built most of these queries, so you will want to thoroughly test them before use. I suppose you could create a procedure that would use EXECUTE IMMEDIATE to create the actual statements to run dynamically, but because queries will receive ORA-08103: Object no longer exists while the move is in progress, I think it is best to control that process manually even if it does mean a bit more time/effort.