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How much worse is encrypting a LibreOffice document with the built-in mechanism than using a cryptocontainer (LUKS, VeraCrypt, etc.) and storing the document in it?

I am more comfortable using the built-in password mechanism that LibreOffice has, but I have a feeling that it is much less secure than cryptocontainers.

I want to protect against, for example, losing a flash drive with an important file, the contents of the file will not be compromised.

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You have to take the different purposes into account. LUKS and VeraCrypt are for encrypting partitions where you may store multiple files securely. LibreOffice password protection is for the document contents of one file.

Metadata like the file name will stay unencrypted with LibreOffice, whereas VeraCrypt or LUKS will encrypt the entire partition and therefore the filename as well.

You have to consider though that once you unlocked your partition with VeraCrypt / LUKS your file is accessible in plaintext to all running programs. When your file is using the LibreOffice password, the programs are unable to decipher the file unless you provide the password. So actually a combination of both is the most secure.

In your flash drive scenario I would recommend to use an encrypted partition, because you are unable to forget setting the encryption on new files this way. You got to be aware of the higher privileges needed for mounting those encrypted partitions and the additional software needed though.

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