If your Apple account is separate and the uploaded backups are untouched by the company solution, then yes (in other words, if file deletion doesn’t sync into your iCloud backup)
Note that the company might use the management tool to block you from connecting personal accounts!
There’s all kinds of options like Microsoft Intune to corporate antivirus + data protection solutions
If my company wipes my Mac through such a system, but I have it hooked to my own personal Apple cloud account, can I go buy a new Mac and restore it?
If your Apple account is separate and the uploaded backups are untouched by the company solution, then yes (in other words, if file deletion doesn’t sync into your iCloud backup)
Note that the company might use the management tool to block you from connecting personal accounts!