test: fix flaky test-single-executable-application-empty #2924

Job	Run time
Build slim tarball	1m 33s
x86_64-linux: with shared libraries	1h 53m 0s
aarch64-darwin: with shared libraries	1h 55m 22s
aarch64-linux: with shared libraries	1h 26m 8s
x86_64-darwin: with shared libraries	54m 49s
	6h 10m 52s

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