Pendlebury will play his 433rd game when the Magpies host the Eagles at the MCG on Saturday, after being left out of the team in two of the previous three rounds.
The Pies drew with Hawthorn and suffered a narrow defeat to Sydney without Pendlebury, after he had starred in the Anzac Day thrashing of Essendon.
McRae has repeatedly defended the 38-year-old's management plan, which has drawn plenty of criticism as the club prepares to cash-in on a huge crowd.
On Thursday, McRae hit back at accusations Collingwood had "hand-picked" the 15th-placed Eagles for the milestone match.
"To be honest, I think that's pretty naive to think we would do that," McRae said.
"We set a plan in place around what Pendles' milestone could look like.
"We're not crystal-ballers, we can't predict the future. There's so many things that have to go in to get here to this game.
"He's been rested here and there or managed with a sore Achilles and other parts. If we put him out there he might've done his Achilles or more.
"There's so many moving parts. No, there's never been a target of certain individuals or competition. That's pretty naive."
McRae wouldn't buy into whether the criticism was "fair" as Collingwood celebrate Pendlebury moving past retired North Melbourne legend Brent Harvey's games record.
"I'm not here to judge fairness. I actually say to my little girl, 'Life's not fair, so get ready for it'," McRae said.
"So I don't live in that space. We're here to high-perform and let the other part be the other part."
McRae also brushed off questions over his boundary-line exchange with Sydney ruckman Brodie Grundy last round, which has come under scrutiny.
In the immediate aftermath, McRae and former Magpies star Grundy both said there was "nothing untoward" in the incident.
But it has prompted debate about whether coaches should be interreacting with opposition players on the field.
"I can't articulate what I said because it was a personal thing. For me it was just a moment in time and we keep moving," McRae said on Thursday.
"If you have a strong relationship with someone I don't see an issue with it.
"I coached him when he first got drafted. I've got a really strong relationship and great respect for Brodie.
"There was nothing untoward and at the appropriate time I might be able to tell you what I said."
Asked whether he had reached out to Grundy since the incident, McRae said: "Is it that big an issue, is it?
"No, I haven't, but I might actually now. I might reach out to Brodie and just make sure he's OK."
McRae prefers coaching from ground level and doesn't plan on changing tack.
"I love coaching from the boundary. There's a real connection to the players there," McRae said.
'I feel there's an energy for me on the boundary line with the team and an ability to instantly react to situations in the game."
Meanwhile, McRae hinted there is "some news brewing" on premiership forward Bobby Hill, who is likely to miss a second straight VFL game this week.
Hill hasn't played an AFL match since last August, having taken leave periods while dealing with personal issues.
McRae is hopeful the 26-year-old goal-sneak, whose partner is expecting a baby in the near future, will return to action at some level this year.
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