The new iTunes (12.7) does not manage apps, this must be done from the device itself, my iPhone in this case.
Can I delete all the IPA files from my MacBook HD?
Yes, you can remove the apps from the Mobile Applications folder in your iTunes library and Transfer Purchases will no longer re-download the apps. However, should the app be removed from your App Store purchased list, the IPA will be the only way to reinstall the app in the future.
This may cause some regret since the IPA that iTunes used to download were special versions of the apps that contain all of the app. Most apps on the store these day have been thinned and when you download an app on the iPhone, it it a thin version skipping parts only needed on the iPad for instance.
If you don’t keep a backup copy of the full IPA and a copy of iTunes older than 12.7 you will lose the ability to reinstall from the full image.
This is not much of a problem if your app of choice neve changes or never gets removed from the online App Store. This also isn’t much of a problem if you upgrade your hardware often. For people interested in running older and not supported hardware and/or abandoned apps or old versions of apps, this can be a substantial problem.