Currently development of SSIS packages is very source-control-system unfriendly. I'll just copy my feedback from the blog of Matt Masson.
Layout is visual, client-dependent information. It can be even regenerated by BIDS/SSDT automatically. It's pretty unfortunate that this information is placed in one file with the actual package logic and human intervention is needed each time the decision needs to be made whether it was a code-relevant change or not.
Comparing to .NET/C# development, Visual Studio guys made a great usage of partial classes and moved the layout, generated by the designer into *.Designer.cs files. BIDS/SSDT would definitely benefit from a similar, modular approach.