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What you explain I understand completely. I know very well that cyberseo/syn cron just simulates site visit.

However, there is nothing impossible here.

Server Cron kicks php, than php checks time, if returned value is time, php continues with heavy feed pulling.

Currently it works exactly like this, BUT cyberseo checks if it is time by minutes back counter (if backcounting has finished, or overdue what is the ASAP stalled feeds problem). It rather should check … What is the time, is it 10:05, is it 11:05, is it 12:05 …., if yes run feed pulls which are scheduled with each hour past 5.

This way no matter if you use server cron or only WP cron, PHP would know exactly when to execute. Currently CyberSEO php runs ambiguously on no exact time. The practice shows it messes it all up.

Scheduling in its nature means knowing exact time. With CyberSEO/SYN you can make it work in exact time only if you run cron each minute.

I dont want to say CyberSEO is not god or anything else is better. CyberSEO has its own advantages, but you can check WPeMatico free version.
Their scheduler works and makes order in all timings.

I did not say PHP executes itself.
I did say:
In 10:05 Cron or a user visit wakes up PHP. PHP asks is time equal to pull feed time, if Yes – pull, if not Die. If scheduling options are at 5 minute increments (who would need less!?!) and a server cron is done every 5 minutes each hour. PHP waking up and scheduling will coincide.

Your script works like 

In 10:05 Cron or a user visit wakes up PHP. PHP asks is time expired (pull time equal or less server time), if Yes pull feed, if No die. And it receives Yes on 20 feeds, so 20 feeds start to be pulled.

This is a huge difference (exactly this pull time LESS server time). The first case PHP executes only when it is told to. Second case PHP executes under condition that is always true (period has long time ago expired) until it succeeds in order to start next back counting period. So if it never manage to succeed, it will keep trying every time cron wakes PHP. This is very bad logic that progressively loads the server. And you know this already. The forum is full with problem posts.

You need to limit feed pulls outside any other time than the EXACT specified time. That has nothing to do with who and how triggers the action.

The condition LESS limits your script from any scalability. Lets say I have 120 feeds to pull. In correct scenario I would spread them across 10 hours. Lets say second feed has bigger latency and huge images. In correct scenario I would not care. In your case that feed will ruin all feeds, because it will be expired, it will expire all other feeds and all will end up in a mess. 

Simplicity and durability is achieved when main use case scenario is perceived. Hence, there will be no 8 or 13 minutes. Only 5 minutes increments. By this logic you have to make the ability for those who would like to pull at 3 minutes 55 seconds. This non sense.

Yes, Cron should be setup to at least 5 minutes. A user can decide depending on his feed pulls preferences.
One user can have 120 feeds and setup a 5 minute cron.
Another user can have 12 feeds and setup 1 hour cron.
This is the order conditions, nothing bad about it. In the case right now the only real working scenario is setting cron to 1 minute, or having under 10 feeds. I think majority of your user base has more than 10 feeds.

Second – the time difference. You are right, usually they are different. But again this is out of the box logic. It is an external system that has its own setup.

The case where an alien cron (cron not local to WP install) is used, is very exotic scenario and this should also remain out of the logic. 

Usually time difference comes in hours, not in minutes. Although a case with minutes is possible. I check my server, WP and server time minutes are 1:1.

If you are that concerned with this time differential, you can check this once and create a variable to compare with pull time instead server time. If you want to cover exotic scenarios, write a cron testing page where cron beacon will be recorded and it will show the user if cron is always late and give user possibility to insert the time differential. However, I think this is not necessary.

Once again I advise you to check how your rivals have achieved it. There is nothing to feel bad about it. SyberCEO is a great plugin with many nice tools, but needs a little fix up. Otherwise, pity, non of the great tools can not be used. For example translation. I turned off 29 feeds and left only one for translation. Now I get all posts translated without random non translated. So it is not Google API problem, its the server time our and peak overloading, because of feed pull congestion.