Base setup modification after HF Installation

[yuvnith]

Scenario:
We have a base setup which has 2 packages
Package 1 with features A, B, C, D
Package 2 with features X, Y, Z

We performed the following steps
Step 1: Install the base setup by only selecting features A and B (only package 1 is installed and version 1 files are copied)
Step 2: Install Hot Fix on top of the base setup (only package 1 related msp is installed and version 2 files of features A and B are copied)
Step 3: Modified the base setup by including all features A. B. C. D. X, Y, Z

Actual result after Modify:
Version 2 files of features A, B, C, D are copied
Version 1 files of features X, Y, Z are copied

Log:

[F2BC:E014][2024-06-06T15:19:18]i201: Planned package: Package1, state: Present, default requested: Present, ba requested: Repair, execute: Repair, rollback: None, cache: No, uncache: No, dependency: Register
[F2BC:E014][2024-06-06T15:19:18]i201: Planned package: Package2, state: Absent, default requested: Absent, ba requested: Present, execute: Install, rollback: Uninstall, cache: Yes, uncache: No, dependency: Register
[F2BC:E014][2024-06-06T15:19:18]i207: Planned related bundle: {e6a583b1-a78f-46c5-b779-57610fc08de5}, type: Patch, default requested: Present, ba requested: Present, execute: Install, rollback: None, dependency: Register

Our SDK failed the related bundle installation as the hotfix is already installed.

Can anyone please provide the expected behavior for this scenario.