Yes that is fine. It is done fairly routinely and is the only way to really obtain fine tuned dosage when the desired dosage is in between the manufactured dosages of set mcg pills.
It takes about 6 weeks for T4 to stabilize levels in the blood. So averaging the two between the two days is basically insignificant over the larger window of 6 weeks or so.
So in essence you are taking the average of 94 mcg per day.
Similarly, if you change dosages, it will take up to 6 weeks for the blood levels to reflect the change, and possibly symptoms can follow even the blood levels by some weeks.
When trying to assess your thyroid status, symptoms should be the main concern, followed by Free T4 and Free T3 levels, and sometimes Reverse T3. Along with that you want to make sure that your Vitamin D, B12 and ferritin are optimal.
So please tell us about all symptoms you have, and post your thyroid related test results and reference ranges shown on the lab report.
On the original question of taking 100 mcg of Synthroid one day and 88mcg the next - yes, people do it, but personally I take a very dim view of doing that. If we assume for a moment that your ideal dose is actually 94 mcg, then that means you are taking too much one day and not enough the next. The way the body reacts to process too much is not the same as for too little - so you have to assume that your body can shift gears quickly every 24 hours to handle this situation. I think that assumption is questionable, at least not proven. More to the point, it is totally unnecessary to get 94 mcg this way because it is NOT the only way to get 94 mcg. You could take one 50 mcg tablet and half of a 88 mcg tablet (all you have to do is break the 88 tablet in half). Another method would be to get 94 mcg capsules made at a compounding pharmacy.
I see from your post in June that you have "anxiety", and feel tired if you take slightly less synthroid. It is my opinion that you are not getting quite enough synthroid. First, synthroid doses are more typically 100 to 125 mcg. Second, if "anxiety" is really elevated irregular heart beat or atrial fibrillation - that can be caused by hyothyroidism. Certainly fatigue can be due to hypothyroidism. Third, your TSH of 3.8 is a little high in June indicates that your body is asking for more. At best, you are getting the absolute bare minimum amount of synthroid. Most likely your doctor(s) and you(?) are afraid of giving you too much synthroid lest you become hyperthyroid which is also associated with atrial fibrillation. But if you search you will find plenty of papers discussing atrial fibrillation and hypothyroidism. You are a long way from being hyper. If you want to experiment, you could add 10 -15 mcg of T3 to your daily 94 mcg T4 and I think your FT4 and FT3 would snap pretty close to mid-point. That's what I did.