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I know that with standard objects one can do AccountId instead of Account.Id inside a SOQL query. Is it possible to do the same for custom objects, say for My_Object__c? Is there a way to reference the Id without using a dot . notation?

I am currently getting the following error if I use the dot notation: The left operand 'My_Object__r.Id' cannot have more than one level of relationships.

I get this when executing the following query:

SELECT

     Id,

     My_Object__r.Some_Field__c

FROM Opportunity

WHERE My_Object__r.Id IN (SELECT Id FROM My_Object__c WHERE Name LIKE '%myobjectname%')

LIMIT 1

Yes. For some custom relationship from child to parent My_Object__r, your Id will be My_Object__c, and you can reference that field in your SOQL query without performing a join/traversing the relationship. (In fact, it is preferable that you do so!)

The place you have to go somewhere special to determine the relationship name is when you're querying from parent to child, where you locate the child relationship name on the configuration of the lookup on the child.

Here, going from child to parent, your relationship name and Id field name are both derived directly from the API name of the lookup field. The Id field is just the lookup field; the relationship is the lookup field with __r.