Best weightloss calculator I've EVER come across.

Ok, so there have been a few questions going out and ill try my best to answer them all...

1. Question on standard recomp - is eating a lot more on workout days really more effective for body recomp than spreading them evenly throughout the week?
You say that you preferably eat 2,000 a day, not 1,600 on rest days and 2,400 on workout days. When it comes down to it; it's all about personal preference. If the weekly calorie total equals 14,000, then regardless of how you spread those calories out the weight loss will be the same. Eating more on workout days can be benificial as you can get more energy to get through a workout, but at the same time it's not necessary.

2. 'Im new to this...it's saying I should be eating more?'
In short, yes. But without seeing your calculations I could be wrong. Myfitnesspal tends to underestimate calories resend for sustainable weight loss, especially in terms of macronutrients values and what we need.

3. What constitutes a workout? Mine could be considered pathetic sometimes.
When it comes own to it, you've got to be honest with yourself. If you only do a few measly workouts throughout the week, maybe a light jog, half an hour of weights and an hour walk, then don't preset your activity level to heavily active...set it to lightly active and that will give you a more reasonable TDEE (total daily energy expenditure)

4. It wants me to eat 1192kcal on a rest day...wtf??
Is that too little, or too much in your eyes? What did you set your weight loss goal for on it?

5. On page 4, it presets 90% fat loss with no consideration for protein intake...shouldn't it depend in protein intake for the amount of fat or muscle lost? Is it possible to maintain TDEE at a deficit?
I had a play around, and it seems to be there's a certain limit to which it says we will lose lean body mass, regardless of how high the protein intake is put into it...it tends to be more about carbohydrate intake for the amount of fat and muscle loss, as long as there is sufficient protein intake. So while I do agree, amount of lean body mass maintained depends highly on protein consumption, the calc is a bit off in that regard.
Your TDEE is the amount of energy you use throughout the day, so yes you can eat at a deficit and maintain a high TDEE. At least, I think that's what you're asking. Say, I burn 2,700kcal on average a day, I eat 2,200 on average per day. Therefore TDEE of 2,700 is maintained while I eat at a 500kcal deficit.

6. Maybe im not getting it, it's telling me to gain 5lbs?
I'm assuming that you're looking on the first page when it has your 'perfect twin' BMI? Ignore that. If not, you've messed up some settings along the way and set it to gain weight.

7. Weight loss of 1lb is not enough! I wanted more like 1.5lbs-2lbs!
Ask yourself this, did you put the weight on at 2lbs a week? No, so why would it be sustainable to lose it at such a rapid rate? If you start losing a lot quicker than 1lb a week, chances are you are losing muscle. Which is NOT good.

8. I put in more workout days, it's telling me it'll take longer to lose the weight?
As above said, that's because workout days would have been set at a higher calorie intake, therefore weekly intake is higher and total deficit drops. Go back to the pie graphs and change your intake a bit lower on workout days.