How to prevent automatic aggregation of contacts
As an Android Developer, I know, that it can be done programmatically in an app:
https://developer.android.com/reference/android/provider/ContactsContract.AggregationExceptions

However, I don't know if there is any contact app having such behavior.

I know one app that has so-called "private" contacts feature - that's contacts that it does not share with Google. It might help you but you'll have to use it instead of the default one:

https://github.com/SimpleMobileTools/Simple-Contacts

Here, for a very small price (half a dollar in September 2019) https://play.google.com/store/apps/details?id=com.simplemobiletools.contacts.pro

Here, for free:
https://f-droid.org/packages/com.simplemobiletools.contacts.pro/