I haven't seen the movie, and the topic is a broad one, so answers must unfortunately also be broad. The era that you are interested in is known as Reconstruction, and you might also be interested in the The Lost Cause, which explores how some Southerners reacted to defeat.

The surrender terms for Confederate soldiers were extremely lenient. As an example, General Grant's demands were:

In accordance with the substance of my letter to you of the 8th inst., I propose to receive the surrender of the Army of N. Va. on the following terms, to wit: Rolls of all the officers and men to be made in duplicate. One copy to be given to an officer designated by me, the other to be retained by such officer or officers as you may designate. The officers to give their individual paroles not to take up arms against the Government of the United States until properly exchanged, and each company or regimental commander sign a like parole for the men of their commands. The arms, artillery and public property to be parked and stacked, and turned over to the officer appointed by me to receive them. This will not embrace the side-arms of the officers, nor their private horses or baggage. This done, each officer and man will be allowed to return to their homes, not to be disturbed by United States authority so long as they observe their paroles and the laws in force where they may reside.

Basically, once heavy equipment and ordinance had been turned over, Confederate soldiers were free to do as they pleased provided they followed the laws of the United States. While a handful of Confederates were punished by military tribunals, the majority weren't. By 1866, anything that had occurred during the War was considered water under the bridge, and former Confederates were generally not persecuted or prosecuted after that period (at least officially; unofficial persecution undoubtedly occurred).

Now for your specific questions.

Has there been any true accounts of confederate officials using their position in the war for either self gain/or straight up respect, even though they lost?

Yes, to the same degree that all humans use past accomplishments for future gain. A respected official is a respected official, regardless of the source of the respect. Most Confederate soldiers would have returned to their homes, which would be located in regions that would have populations that were supportive of the Confederate cause. Therefore they would, on average, be supportive of the people that had fought for that cause (regardless of the outcome).

Was there any side effects to that?

Plenty. Civil War ties and politics dominated this time frame, and it was a period of massive changes. On an individual level this could manifest in some fascinating ways. A fun example is the Hatfield-McCoy feuds. While not specifically caused by the Civil War, it's not a coincidence that it flared up at the end of the War after soldiers started returning home, nor is it coincidental that one family supported the North and the other family supported the South.

Were the Union tolerable to confederates, kind of (and apologies for not using academic terms) "flaunting" their rank even though they were confederates?

As stated previously Union terms for Confederate surrender were extremely magnanimous, especially when one considers that the Confederacy was a rebellion and treason is a crime typically punishable by death. Nonetheless Confederate actions weren't always thankfully gracious. Many of the outlaw gangs of the "Wild West" were simply Confederate guerillas (known as "bushwhackers)" that refused to retire when the war ended. You might find Archie Clement, the James-Younger Gang, the Mason Henry Gang, and William McWaters all to be of interest.