Six-time Ballon d'Or winner Messi sent shockwaves through world football by handing in a transfer request at Barca this week.
City are viewed as frontrunners for his signature, with Messi reported to have called Guardiola – Barcelona's head coach during a decorated period between 2008 and 2012 when Messi became widely regarded as the finest player on the planet – to give him notice of his intention to leave the club he joined as a 12-year-old.
Disputes and negotiations over how much of a fee Barcelona can collect for a player who officially remains not for sale, indeed whether they are entitled to a fee at all, are set to rumble on next week.
Unzue, who served as Guardiola's goalkeeping coach at Barca before working as an assistant to Luis Enrique between 2014 and 2017, hopes a resolution that ends with Messi in Manchester is reached.
"On one hand, if he leaves Barcelona, I would love that he goes to remember old times with people he already knows and has felt a shared success with," he told Stats Perform News.
"I hope he goes to Manchester City; I say this sincerely. I am sure his decision will be very tough.
"Also, I am sure he keeps a great memory of that period with Pep because everyone has grown up alongside Pep.
"This is a reality, not just the players but everyone who has worked in the staff too. I speak for myself, but I have felt and heard that from others."
Messi requesting a move only amplified the noise of superclub in chaos, with sporting director Eric Abidal following head coach Quique Setien out of the door in the wake of the humiliating 8-2 Champions League quarter-final defeat to eventual winners Bayern Munich.
Ronald Koeman was installed as Setien's successor by under-fire president Josep Maria Bartomeu, although claims the Dutchman swiftly told Luis Suarez he was surplus to requirements apparently only exacerbated the Messi situation, which appears to have been brewing for some time.
"I think it is complicated because he is an intelligent person with a great personality, although very introverted," Unzue said.
"This is not in the heat of the moment. I am sure he has absolutely evaluated the circumstances. I think he deserves and has earned the right to make his own decision.
"We can talk about whether it is the best or the worst way. I will not say anything because I do not know what happened within the club and between the people involved. He has earned that right."
The now infamous burofax, sent by Messi's representatives to Barcelona asking to leave, sought to invoke a clause in his contract that allows him to walk away for free at the end of each season.
Even though the terms of that clause are now up for debate given how the coronavirus pandemic distorted the schedule, Unzue feels it shows Barcelona were willing to grant Messi the autonomy over his future he is now trying to exercise.
"The contracts he has signed during the last years said this," he added. "The club has left a door open to give him the opportunity to decide.
"He understands he can find other motivations, other team-mates in another place, a change that sometimes is necessary."