An entity marked with the flag readOnly=true is not tracked for updates anymore but it is still possible to insert or delete rows, as explained in the documentation.

The doctrine:schema:update command will still take the table into account to update the schema.

In the answer to the question "Ignore Doctrine2 entities when running Schema Manager update" There are 3 valid options to ignore entities in schema updates.

schema_filter

schema_filter is not made to "filter" entity but to filter db table from doctrine awareness.

Here is an example:
Assuming you manually create a table that is updated from a custom raw php cronjob called view_booking_by_customer_per_year, this table is not used by your code in your project but is used for data analysis.

This is a typical example, you don't want to generate such a query every time you update the schema.

DROP TABLE view_booking_by_customer_per_year; // NO I DONT WANT THIS

So using schema_filter you can tell doctrine to ignore this table in his validation and update process.

Try to create a random table using raw sql and use doctrine:schema:validate. It will show database is not in sync error. Once I put it in schema_filter the error no longer occurs.

It work for doctrine:migration:diff and doctrine:schema:update

schema_ignore_class

However, if you want to avoid generating entities within the database, you can find that from the link in Ernesto's answer:

schema_ignore_classes:
   - Reference\To\My\Class
   - Reference\To\My\OtherClass

Only works from Doctrine 2.7 version. You can find the complete example here: Ignore Doctrine2 entities when running Schema Manager update

Use Doctrine Migration

I strongly advise you to use doctrine:migration:diff then doctrine:migration:migrate instead of doctrine:schema:update to perform change on database . It's ok for local dev, but when in production it is a very bad practice.

https://symfony.com/bundles/DoctrineMigrationsBundle/current/index.html