Unless you are sailing in very light winds, it is generally desirable to keep the sail's CE (and thus usually also the boom) as low as possible to minimize their heeling leverage. In really light winds there may be a bit more wind to capture at a higher altitude above the water, but most of the time, low is how to go on any boat with such limited stability. I wouldn't worry much about which vertical configuration for the yard's angle is more efficient. There are so many variables going on as you sail, that a two second lapse of concentration influencing the heading in relation to the wind direction, heeling control or sail trimming can be a bigger factor.
Nobody sails perfectly, so it's always going to be a mixture of things you did well and a few things which you didn't do so well. That generally makes a lot more difference in your overall VMG (velocity made good, or how much of your effort is actually moving you toward your target). Mechanically, if you do raise the yard to be more parallel with the mast it will also be moving the sail's center of effort forward, which may require adjustment of the fore and aft leeboard position in order to maintain good helm balance (best determined by experimentation out on the water). We did that for one of my customers when he wanted to add a jib, which doesn't work on a lateen in their normal configuration.
However...... aside from all this, avoiding getting hit in the head with a small boat's boom while tacking or jibing is a technique thing, not a rig configuration thing. If you learn to tack and jibe these small, low rigs properly, you will never get hit in the head - no matter how low the boom is. There are three phases to this sort of tacking or jibing and they are all just simple ways to control the process. (1) As the sail and boom are coming inward toward you when starting a tack or jibe, follow them in by trimming-in the excess mainsheet which is being created. You are not trying to pull the sail in, let the wind and heading do that. You're just monitoring and taking care of the slack line which is being created. (2) At a certain point during the tack or jibe, the sail will briefly align with the wind direction and go slack. Sometimes it will hang there and wiggle for a second or two. It is at this point, when there is no pressure on the sail that you just grab the boom and pass it over your head. There is no law that says you can't touch the boom while tacking or jibing, and learning to do so when it goes slack will make your tacks and jibes a lot smoother and easier on your head. (3) The slack period is extremely short and after you pass the boom over your head, the sail will start to fill with wind again and you simply play out the mainsheet under control as it does so, following the boom out. I always called this maneuver a "forced cross" though in reality you aren't forcing anything. With a little practice, your tacks and jibes will be consistent and smoother with no danger of getting beaned by the boom, and without increasing the heeling force the way a high center of effort would.
The other factor to be aware of (and get good at, especially for tacking) is nailing down the details for tacking your particular boat, as they are not all the same. How much speed do you need to carry into a good smooth tack? What are the best tacking angles heading-wise? How much rudder do I give it to turn the boat without stalling it and at what point during the tack do I need to start applying rudder? Do not be surprised if it takes a whole season or more to really get to the point where your tacks all work and are all smooth. Long, skinny boats like canoes and multihulls can be rather unforgiving of tacking errors until you get the rhythm down for that specific configuration.
The reef-able lateen sail with the clew raised high, making room for a boomed, self-tending jib