Being pardoned does not mean you are innocent nor does it erase the crime. There is an upside and a downside.
UPSIDE
Your civil rights are restored. You can vote, run for office, own a gun, serve on juries.
DOWNSIDE
You can no longer hide behind the 5th amendment. If you refuse to testify you will be jailed for contempt of court. So being pardoned opens you up to testifying UNDER OATH about whatever the authorities want to know. Whatever it was you were hiding. Whatever it was you wanted to keep secret. That 5th amendment protection is gone forever. Additionally if a prez pardons wantonly and promiscuously and willfully he can be impeached. ABUSE OF POWER is an impeachable offense.
So if Manafort is pardoned he can be compelled to testify against donjohn and spill his guts. What is the benefit/gain for don to do that?
The don can only pardon folks for FEDERAL CRIMES, not state. It isn't a carte blanche power. It ain't a limitless credit card. There are rules.