Lol.. what you miss could fill a novel.
First, no one said the company was the sum of employee cost. If the company doesn't turn a profit, there will be no employee cost because it will not be in business. If the subsidies are the reason the company is making a profit and still open, then it is entirely reasonable to connect the subsidies to their pay.
Second the only thing not logical is your thinking. Sure they could get a job somewhere else. But that ignores the fact that they wouldn't be working for that company. It also ignores the fact that unemployment is not zero. Their reemployment elsewhere would either displace another worker if all things otherwise was the same or some other company would expand due to that company no longer being in business. That means they are not employed or the subsidies are depressing other businesses.
The rest of your post misses the fact that if all other costs caused them to not be profitable enough to stay in business without the subsidies, the jobs would only exist because of the subsidies. Again it is completely reasonable to connect them.
It is not a complicated process at all. If the company can not make money without the subsidies, it no longer exists. Those jobs no longer exist if they were even created in the first place. You can try to hide or ignore that all you want but it doesn't change anything.