Is there any reason why the left hand holes and right hand holes need to be completely aligned at the top of the flute.?
As a beginner I feel more comfortable with the left hand holes aligned away from me and the right hand holes towards me with an angle of about 30 degrees between them.
Thanks
Go for it! I do the same thing.
It’s most important to make your hands completely comfortable, meaning no tension either holding the flute or moving your fingers on and off the holes. Set the center sections up for this, the adjust the headjoint to give yourself a bit of up and down flexibility without having to change your hand position.
Cheers,
Rob
That’s why some flutes (mine, for instance) come apart between F and G so I can get the allignment you seek. I must say, however, that even though everyone is different, I question those who play around overmuch with the tone-hole or embouchure allignment. Seems to me that it encourages bad habits in how the flute is held and played, but I could be wrong on this. The reason I say this is I was at an event a few weeks ago where I met a flute player that wanted to try my flute. He had an Olwell that he let me try, and the head was turned so that the embouchure was almost vertical. He was a fine player, so I suppose it doesn’t matter, but it just seems to me that it shouldn’t be necessary.
A flute with a joint between the hands allows you to easily make adjustments to the hole alignment.
I come from a modern flute playing background and for some time I kept with keeping the emb hole in line with the tone holes and since I was playing a Pratten model I had little choice with the tone hole alignment. The body is one piece ergo they are all aligned.
I had been prompted by a number of sources, in person by good players of this type of music and by historical record, to move the centerline to as much as the outer edge of the emb hole to line with the inner edge of the L1 tone hole. At first I thought it so much bullsh*t until I took time to investigate it functionally. I found it to be useful advice. I play a vintage Rudall now and it does afford me a better tone, greater control of tone color and improved my ability to play this particular instrument in tune.
You’ll find any number of different opinions about what may be best but I think the very best advice is to pick a position that is comfortable and stick with it. There isn’t really any “correct” form only that which affords you the most advantage of air control and the least amount of injury in repetitive motion. Sit up! 
Terry McGee has an interesting write up on Mr. Nicholson’s ideas of alignment that can be witnessed by how his “improved” flute were made.
http://www.mcgee-flutes.com/Nicholson's%20Flute.htm
I actually twist my L/R joints totally opposite of what Nicholson recommends so as always with this sort of advice, your mileage may very.
Cheers!
A
“A flute with a joint between the hands allows you to easily make adjustments to the hole alignment.” Doug Tipple.
I don’t think it’s a good idea to encourge people to smoke weed when playing the flute. You are fooling yourself if you believe your playing sounds better when you are high.
What’s a nice flute like you doing in a joint like this? 
Don’t knock it till you’ve tried it. Cough, Cough…
There is no acoustical disadvantage. Look at any modern wind instrument including modern flutes and you will see some tone holes located around the circumference of the instrument. For a simple system flute then, where the finger holes go is simply a matter of comfort and preference.
Casey