Alon
It just feels like you are afraid of trying new things. You prefer to ask on the forum "what would happen if I do this or that", instead of simply testing yourself.
Worst case scenario - something will not work, undo the changes and move on.
.
About the save size - have you tried viewing your ".alon" files? Create one object instance, save to .alon file. Then rename the file to .json and open it - you can upload it to any online JSON viewer website, or simply open with Firefox. You will see that there is nothing scary there, just some information about your layout, layers and object instances. You can actually find object's instance variables and their values, and will see how much space each variable is using.
This can help you to get better understanding of how things work in Construct. Besides, you may find something in the file which will help you to optimize and decrease the save size, for example some objects that don't need to be saved.