Is MD5 still safe to use?
To check that a download arrived whole, yes: accidental damage changes the hash. To prove a file was not tampered with, no, since someone can build a second file with the same MD5. Ask for SHA-256 when the source offers it.
What is the MD5 of an empty file?
It is d41d8cd98f00b204e9800998ecf8427e. Seeing it means what was hashed was empty, often a download that failed before its first byte arrived.
Can I paste what certutil or Get-FileHash printed?
Yes, as it is. The three lines of certutil -hashfile setup.exe MD5 and the table row of Get-FileHash -Algorithm MD5 both work: the hash is found in either, capitals or not, and compared with yours.