The $99 buys a certificate that Apple can revoke if (for example) you were using it to sign malware. The revocation of your certificate would prevent your malware from running on any Mac connected to the internet [0].

To me at least, that feels materially less dangerous to run than an unsigned app. Whether or not the system is effective, or if that's worth the $99 is obviously up for debate.

[0] https://eclecticlight.co/2020/10/28/code-signatures-1-how-th... (Search for CSSMERR_TP_CERT_REVOKED)