"Remove from CRM" means "Also remove from CRM," i.e. delete the lead not only from Marketo but also from whatever CRM system you've synced with Marketo using a native connector (SFDC, Dynamics, etc.).
In fact this checkbox confirms that Marketo and CRM are different.
They are. Please read the docs.marketo.com for this function.
This is a flow step that performs an Action on the Lead. It is giving you an option to also delete the Lead in the synced CRM, if you want. There are tons of threads on this, so do a search if you are curious.
To be more specific for your comment --- this flow action doesn't care about the Lead Source. You must select the leads you want to Delete with a smart list, only there should you determine the Lead Source or "System Source"
You asked and easy question, and it has an easy answer.
Is Marketo a CRM? No. It is not a CRM.
Bonus answer: SalesForce is a CRM, Microsoft Dynamics is a CRM. Marketo is a Marketing Automation System that can optionally, send data to a CRM. The option you mention simply allows you to not only delete from Marketo, but gives you the choice to delete from the CRM you have Marketo connected to (if you are using one), like Sanford said.