Number of databases on a server. Should I try to consolidate these objects together?
Best practice is what works best for your organization.

If you're going to discuss this with your boss, who has a certain way of doing things, then you need to plan out the discussion in terms of a business case.

So, first: 
Rank the following twice each, in terms of What's important to you, and what's important to your boss.  If these rankings are the same, you need to re-evaluate; that's pretty unlikely


Maintainability 


via the GUI?
via handwritten SQL?
via automated SQL?

File count on disk
Cross-database queries
Cross-database permissions


Remember, EXECUTE on DatabaseA allows the object executed to access other objects in schemas with the same schema owner; however, going cross-database changes the rules

Quickness of the initial, first draft of a solution
Quickness of adding dozens of followon, similar solutions
Quickness of adding dozens of followon, identical solutions
Quickness of making changes to dozens of already existing similar solutions
Quickness of making changes to dozens of already existing identical solutions
Ease of investigating why solution A6 is not quite acting like solution A23, when they "should be" the same
Ease of restoring the entire set of databases somewhere else
Separation of data so customer A's data is not mixed with customer B (often a contractual requirement)
Ease of moving the entire set of Agent jobs somewhere else
Overall performance of ALL the solutions at once - profiler, extended events, indexing, monitoring
Foreign keys 


which CANNOT go cross-database



Essentially, most of this boils down to: If you want one-off results as quickly as possible for each one-off unique thing, a separate database makes sense, but they should be destroyed when they are no longer required.  However, long term, you're going to have hundreds of databases; is that desired?  Or required, perhaps, due to contracts?

I would say that the arguments to consolidation are firmly around foreign keys (data integrity), identicalness of solutions (data integrity), and doing stuff by hand.  The latter should be replaced with automated techniques which can just as easily handle 500 databases as 2, so I would ignore that.

Again, know what's important to your boss; if consolidating is a solution that is superior in terms of what's important to them, you've got a good potential for a successful argument.  If not, you don't.