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Yes, it is a bit strange. I'm a native speaker and I would have said "in a single PHP file" too.

A lot of non-native English speakers have difficulty with articles (a, an, the, etc.).

I'd say the word 'single' is redundant as it a PHP file. How about "Database management in a PHP file"?

But then it doesn't have as much impact emphasising the simplicity of it.

It is odd. "a file" almost feels less specific than "a single file", even though the latter is technically redundant.

I've added "a" between "in" and "single", it started sounding weird to me some time ago as well. Thanks for the suggestion. Can you please propose a correct wording for the second sentence?

It's from Jakub Vrána, a Czech developer. Czenglish sucks.