If you read the your quote above, it kinda says it all. For most people, alternate picking at “moderate” speeds is difficult. So elite level picking is going to be extremely difficult to nail 100% of the time. Watch any Dream Theater performance and you will see Petrucci flub some notes or not quite keep up during the most demanding technical parts- and thats Petrucci who only needs to worry about playing like Petrucci and has practically all day to play/practice and on tour plays most nights. Judging by the above video, I have to agree with @JonJon and say that I think you feel the problem is bigger than it really is. Your playing is excellent, don’t grow a problem that isn’t likely to be a problem in reality - being able to maintain technique to a high level with no more than an hour a day? Bloody hell, i’ll sign up for the disease you have lol!
Also, make sure you judge your playing from the point that you are warmed up, not as soon as you pick up the guitar. It is very easy to get frustratedout of context
As @JonJon points out, take a week of guitar and see how you fair, you might find that when you return, your playing benefits. At worse the drop off of technique will be about the same as a day’s rest and that an hour is all it takes to get back into the groove.
If indeed it is a “phase” that will pass, then keep practicing and let it arrive. You cannot speed that up, it will either happen or it won’t. It may happen in 5 months or 5 years - it doesn’t matter.
Good luck on your quest my friend!