Chris,
Toilet
As long as you get antifreeze through the system, or remove the water in the system, you should be good. Be sure to get antifreeze into the holding tank(s). This might be a wild guess depending on how well the system gets emptied during the last pump out. I usually put a couple gallons of RV antifreeze through the toilet and into the tank. I have connected a hose to the toilet sea cock fitting and used the toilet pump to draw RV antifreeze into and thru the toilet. While you are winterizing the toilet, pour some antifreeze into the floor drain to protect the shower sump. I usually add enough to make the pump run twice.
Air Conditioning
That should work as long as you have antifreeze in the a/c system's water pump and plumbing. You might to look at the a/c unit to see if the drain pan has drained.
Fresh water
Blowing out and completely draining a water system is always an option. If there is no water it will not freeze and break a line or component. Getting all the water out of low spots can be a challenge. I run the water out of the tank, drain the water heater, then add 8 to 10 gallons of RV Antifreeze. I remove the transom shower head from its hose and use a 1/2" male pipe thread to male garden hose adapter fitting to connect a garden hose to the transom shower hose. I can put the other end of the garden hose in the fresh water fill fitting and open both hot and cold transom shower valves to circulate antifreeze through the water heater and most of the system. I run the galley and head faucets into a gallon jug to get antifreeze in those lines and not waste antifreeze. While you have this hose set up you may be able to use it to flush antifreeze through your a/c system. I added a small in-line valve to the end of the hose and whatever adapters so I could control flow at the end of the hose rather than going back to the transom shower valves. Keep in mind that the water heater holds 6 gallons. Add a little for the water tank and plumbing, and you might need more than the 3 gallons. Most of this antifreeze can be re-collected or drained back into containers either this fall or next spring for winterizing next year. The down side of using antifreeze in the fresh water system is the possibility of tasting it next year. Four Winns recommends using a bleach solution in the spring, followed by a vinegar solution. Repeat as needed. Another option a friend in Alaska told me about was to use a gallon (or more as needed) of the cheapest vodka you can find. Of course, next spring all the neighbors will be showing up jugs of orange juice to "help un-winterize" the water system.
You mentioned the water heater by-pass. Is that for the engine coolant side of the water heater? If your shop is winterizing the engine, make sure they know what you have done and what you have not.
To minimize the risk of not removing all the water from the engine cooling system and fill with automotive antifreeze. I drain exhaust manifolds, pull both hoses off the raw water pump, and lower the engine flush hose at the right front corner of the engine to get most of the water drained. Then I rig a 40" or longer plastic tub with a bilge pump clamped in the tub and a hose to the muffs. An old 2 wire extension cord long enough to reach the batteries with an inline switch supplies power. I tape a drip collector to the bottom of the boat stern to direct antifreeze back to the tub. I add 7 or 8 gallons of antifreeze to the tub, turn on the pump, and run the engine for several minutes to get a little coolant temperature. The antifreeze can be either removed in the fall or in the spring. I re-collect the antifreeze to use again next year. I might lose 1 or 2 gallons each year in residual antifreeze when I flush it out in the spring. Most communities recommend disposal in the house drain system.
Hope this helps. Gary