I think the experiment might has some mistake, but in general, it works.

6. Sample No.
Keystore
Code Modified
1
keystore_file_1
Original code
2
keystore_file_2
No
3
keystore_file_2
Yes

18. 3,360,586 – 3,360,376 = 210

19. 3,334,868 – 3,334,658 = 210

21. The diff result of AndroidManifest.xml (sample1 and sample2).

22. The diff result of AndroidManifest.xml (sample1 and sample3).

23. The diff result of apktool.yml (sample1 and sample2).

24. The diff result of apktool.yml (sample1 and sample3).

25. Take a look at the smali code (sample1 and sample3).

26. Take a look at sample1 and sample3.

27. Take a look at sample1 and sample3.

28. Take a look at sample1 and sample3 (.apk).

29. Take a look at sample1 and sample3 (after extract).

30. Take a look at sample1 and sample3 (.dex file).

31. Let’s look back to our test sample:
Sample No.
Keystore
Code Modified
1
keystore_file_1
Original code
2
keystore_file_2
No
3
keystore_file_2
Yes

32. Let’s look back to our test samples and make some conclusion…
The different stuffs at each phase (based on sample1):