"At this stage" in corporate speak
Solution 1:
The phrase at this stage has no inherent negative connotation. Just as with at this point in time or at the current moment, these phrases temporize to shirk responsibility, usually in the corporate world.
In the first example you give, whoever declined the application is avoiding finality by hinting that the person might be accepted "if circumstances change".
In the third example, the company hints that this policy may only be temporary. Perhaps employees will accept the onerous policy if they think it is only temporary.
The question of why people use the phrase is subjective. In a corporate environment I suspect that people use the phrase because that's the template and usually employees have discretion in how they communicate with customers, especially in the service issue.
In medicine, in contrast, we use such a phrase to emphasize the incomplete and evolving nature of our understanding of the issue. "At this point in time it does not look like cancer, but we are waiting further test results." That has a side effect of protecting us from Monday-morning quarterbacking.
Solution 2:
It's not part of the meaning of the phrase -- I think it's just a tendency. But it's not a fully coincidental tendency. I think there are a few reasons for this.
- "At this stage" seems to be an excuse, sometimes. "No, the drug is not ready for human testing... yet. It's just too early, we're not actually doing anything wrong."
- It could also be providing hope, as another way of softening the blow of bad news. "Sorry, your application has been denied, but there could be an appeal or something."
- It's sort of sanitary. It makes it sound like your answer has come out of a computer, and that there's nothing people can really do about it.
But, there's no reason it can't be used for something positive. Imagine people are talking to a potential investor: "At this stage, our company is valued at $8 million!" could be very good news, especially if this is an early stage and you expect to grow.