I uncertain what you mean by an endotracheostomy. That translates into placing a tube through the mouth or nose (endo) into the trachea, but ostomy refers to a creating an opening surgically. There would be no need for a stoma to get to the trachea. Maybe this is some new procedure I haven't heard of, but I am guessing you are thinking of oral intubation versus a tracheostomy.
I was orally intubated for three days before the tracheotomy was done and it was pretty awful. They kept me pretty much zonked but I remember a very sore throat at times I was awake. It requires having the tube anchored with a strap around your head and tape to prevent you from pulling it out in your sleep or coming out when you cough. Patients who have endotracheal tubes while in the hospital have wrist restraints on to prevent them from pulling out the tube. You can certainly be suctioned through an endotracheal tube but it passes through the vocal cords and prevents any speech or sound. Any patient I ever had who was intubated and thus had an endotracheal tube and was considered likely to need the tube for more than a few weeks was given a tracheostomy to prevent damage to vocal cords and for comfort.
It is also possible to suction through the nose with a regular suction catheter and no endotracheal tube. That is generally reserved for use while waiting for a tracheostomy to be done to make it easier to remove mucous.
The tracheostomy is far more comfortable. Although the care of the stoma is a big deal in the hospital post op, once you are home it can be reduced to simple soap and water wash and rinse in the morning. It does not interfere with speech or swallowing if you are able to speak or swallow before being trached. ALS however, will in time take away those functions even with a trach. Tracheal suctioning will be frequent at first as your body adjusts to having the trach. Later it will vary day to day from every couple of hours to as little as 4 or so times in 24 hours. Tracheal suctioning causes a strong cough that helps bring the mucous up into the trachea for removal. Good hydration is critical for keeping the mucous thin and preventing thick mucus plugs. A feeding tube is eventually necessary for this.
Suctioning is scary at first but not painful. You may get too short of breath to tolerate suctioning long enough to get the mucous all out but suctioning can be interrupted to let you breathe, or put you back on BiPAP, or give you breaths with an ambu bag. In time you will be relaxed and able to tolerate longer suctioning without a freakout! Anyone, family, friends, private help, can be quickly shown how to suction and with a few opportunities to do it with supervision, they can take over. A nurse is not required for suctioning, but an agency hired nursing assistant is not allowed to.
Mucous that accumulates above the balloon cuff when swallowing gets bad would be mucous drainage from your nasal sinuses. Most of what accumulates above the balloon is saliva. There is no way that mucous or saliva or food or drink that accumulates above the balloon can "overflow" and get into the lungs unless the balloon is deflated. Suctioning right after deflating the balloon will catch the accumulation before it can drain into your lungs. Keeping the balloon inflated prevents talking but not swallowing. It only needs to be inflated all the time when your swallowing is impaired significantly. Even then it can be deflated to allow prompt suctioning to remove anything that has accumulated above the balloon.
A trach is an excellent way to remove mucous when your cough is too weak. It can be used with a cough machine or suctioning, whichever is more effective and convenient for you. You can plug the trach between suctioning if you want, and that can help prevent respiratory infections because your nose, mouth, and upper airway act to trap dust and even bacteria, humidify, and warm the air before it reaches the lungs.
The one danger of having a trach is that it is so simple to attach you to a ventilator if you end up in the ER with a severe respiratory problem. If you do not want to be put on a ventilator in a situation where you are too out of it to say or indicate "No", all your caregivers need to know that, and have a copy of your living will or Medical (or Durable) Power of Attorney to show the ER staff.
I have had a trach and vent for 16 years. I don't consider a ventilator a good choice for anyone with rapidly progressing ALS, but for moderate or slow progression it can add good quality time. A trach alone is a good choice when a cough assist machine combined with good hydration, and guafenesin, a mucous thinner available as an expectorant cough medicine, isn't enough.