The Maximum Upload size is '50MB' for a web-application, will it be the same for the site-collections underneath of that web-application?
Yes, the limit is for everything under the webapp.
If you plan on increasing it significantly, you may also need to increase some other settings in IIS and/or SharePoint to make sure connections don't timeout.
In IIS: Connection Timeout limit
See this post for some good insights on this. It is old, but not outdated I think.