test: mark linux job user override tests as flaky

[YutongLi291]

What was the problem/requirement? (What/Why)

The linux job user override tests pass consistently on my local workspace, but fail most of the time. I believe it may be due to differing instances used.

What was the solution? (How)

Until finding a permanent solution, marking the tests as flaky.

Also changed the command to change back the config file, so that the test can properly retry if the test is flaky.

What is the impact of this change?

Less noise in the tests

How was this change tested?

hatch run e2e-test```
### Was this change documented?
No
### Is this a breaking change?
No
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[sonarqubecloud]

Quality Gate passed

Issues
0 New issues
0 Accepted issues

Measures
0 Security Hotspots
0.0% Coverage on New Code
0.0% Duplication on New Code

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