I think it does make sense to plug a shop app in the project rather than making something from zero, if the project has that much need for customization than it would make sense to use a more lightweight app.
Same question could be asked if it make sense to develop my solution using a framework like django or to make my own?
Either way even a more complete solution like satchmo shouldn't be a burden to integrate in your project, just don't try to copy the code and change it, (you could miss future updates or buy the headache to merge your fork all the time) rather you can easily plug in.
for example:
If you need some custom fields in the product model, instead of changing the shop model you can create your own in your models.py with the extra fields you need and add a foreign key to the shop product model.
success