CRM 2011: Customization First or New Solution First?

I've just started working with CRM 2011 a few weeks ago and I have a question about building solutions.  The company I am with has been using CRM for the past year or two and some of the project managers (non-developers) have made a number of customizations and they purchased a customization from a thrid party. So now I come along and I am looking at CRM customizations, adding JavaScript, adding plugins, etc., etc. and have noticed that their approach has been...

1. Modify things like entities, ribbons, sitemap, etc. directly. 
2. Keep a list of changes as notes. 
3. They leave the "new_" prefix and add something like "_abc_" manually in the field names.  So you end up with fileds named new_abc_firstname.
4. When they are happy with the customizations, they then create a solution and select the default publisher and then add all of the items that have been changed.
5. Then they deploy this as a unmanaged solution.

However, after working through LOTS of training videos and documents, I am finding that most suggest NOT taking this approach.  They suggested..

1. Create a new solution
2. Create a new publisher and modify the prefix from "new" to something related to your company.
3. Add items to your solution that you wish to modify.  Modify those from without the solution, not directly on the default solution.

So my question is... what do I do at this point?  They have a lot of customizations against the default solution.  But I want to do this correctly and build solutions, new publishers, etc.  Am I going to run into any issues here?

Also, we are going to eventually have to migrate from CRM 2011 to CRM 2013.  We run CRM on-premise.  So am I going to run into any issues with all of these customizations, the 3rd party customization solution we purchased, plus all of my new solutions? 

Are there any negatives/positives to making customizations directly against the default solution versus making the changes in a new solution with a new publisher?  I would like to provide them with a list of negatives in regards to making customization changes using the default soluiton and default publisher, if in fact there are negatives.  But I would also like to explain why I we should continue doing this going foward.     

Any thoughts, suggestions, or comments are much appreciated.

Best regards,

Jon Gregory Rothlander