@jonallenaz I am facing a very similar problem, but with forms in general (Custom Item Forms in our case) - particularity around Subsists/Fields.
We have an App that deploys a Custom Non-Inventory/Service item form, and the DEV account that we built the form on happens to have Advanced Rev Rec, Credit Card Tracking, etc features all turned on. We also deploy Sales Transaction forms, 1 X Estimate, 1 X Sales Order, 1 X Cash Sales, 1 X Invoice. When we used SuiteBunder we can install to accounts with "Estimates" deactivated in Setup > Company > Enable Features or with Advanced Rev Rec disabled. The bundler doesn't seem to care about this, and will perform the install and the components lay dormant until said feature is activated.
SDF Issues
SDF on the other hand displays a massive list of errors. We haven't yet tried it, but I suspect "Subsidiary" fields may cause an issue when deploying to Single Company accounts.
Even where the manifest has the feature "required" flag set to "false", SDF still seems to yield many errors