Honestly, just ignore what MFP says and if you go into the red. It's a basic algorithm and works just find for regular Joe but it terrible at customising. Is it possible it's a 40-20-40 split? 'Cause that's what it looks like. Also if you're in a deficit, that will affect your algorithm so you won't be able to get it up to those numbers without the % being whacked. Did your trainer say whether you were working towards gaining muscle or recomposition? Gaining muscle requires a small surplus as you need more calories going in than out to feed the muscle. Recomp is trying to maintain/define what muscle you have while losing body fat, which requires a deficit. Again, all these factors might explain why you're having trouble with the algorithm.

I'm not a lifter but I kickbox, as in training for belts/to compete, so take what you will from my experiences but everyone is different, i.e. I am pretty lean/small, physique-wise so what is required to maintain my shape is not the same as maintaining a lifter's shape. And I have never paid attention to the 30 minute window . You can consume protein a few hours after your workout and it's fine. Logically speaking your body doesn't just go, 'oh...protein? I needed that an hour ago' and chucks it out. No. If you're fine doing what you're doing now then keep at it, but don't feel like you're tied to it. You can even take your protein before you workout if you want to. I tend to consume as much protein as I can throughout the day (chicken on a stick!), helps with feeling full, and maybe have a protein bar, if I have one, on my way home or have a protein shake when I get in if I'm not up to my numbers.

Carbs serve the purpose of energy. Some people feel that they need to workout fasted so that they can burn their energy stores but I have never been able to train without eating. My blood sugar goes through the floor and while I haven't passed out yet, there's still time. I eat my dinner roughly two hours before a session as I train two consecutive hours most days and I eat about 600-650cals*/at least 100g of carbs and then I have a small carb-y snack 10 minutes before the start to push me up to about 800*cals/another 30/40g. Without carbs, you can't think for poop and you'll know when you haven't had enough because your brain will be like swiss cheese for trying to retain anything. I can end up over 300g of carbs on a training day and that's completely fine. It also means I generally don't get hungry after working out. Again, play around with what makes you feel full. Maybe it's protein, maybe it's wholemeal/grains (pasta, rice, quinoa, [sweet] potatoes, volume foods like vegetables), that's down to you. Maybe set aside some calories so you can have a snack after you train, maybe some Greek yoghurt?

Definitely come back and let us know how you get on!

*I'm tall and in maintenance so my calorie count will naturally be higher.