"I think they were somewhat frustrated that it went as far as it did without consultation, and we respect that," Penn told 9News.
"We are all about inclusiveness, so we will continue this theme."
Penn confirmed Manly plans to wear a pride jersey again next season and said the seven players in question have suggested they will get involved.
"Yes, that's the message they were very clear on — let's work together," he said.
The seven players have since been asked not to attend tonight's Round 20 clash with the Roosters at Brookvale Oval match for security reasons.
The boycott sparked a widespread backlash over the past few days from rugby league circles including former players, current players, the openly gay Manly legend Ian Roberts, former English star Keegan Hirst, who came out while still playing, Roosters coach Trent Robinson as well as entertainers, and other sports and social media stars.
Penn said the players are prepared to sit down with Roberts and have a discussion with him.
"The players we met with are keen to talk to him, and get their message across and they want to hear from him," he said.
Coach Des Hasler admitted to a "significant mistake" on the club's behalf and, despite reports of three of the players wavering on their stance, all seven players would be unavailable.
Hasler couldn't answer one question during the press conference after he admitted: "None of the coaching staff or the players had prior knowledge of the jersey."
He was later asked why they hadn't been consulted, to which Hasler replied: "You'll have to talk to management about that, I can't answer that."
Manly named a decimated squad of 20 players on Tuesday.
It includes debuts for wingers Pio Seci and Alfred Smalley, and Zac Fulton, who is the grandson of club legend and Immortal Bob Fulton.
It will also see the club debut of James Segeyaro, who will play his first NRL game since 2019 after a drugs ban, and Morgan Boyle's first game of the season.
One-gamer Kaeo Weekes and uncapped James Roumanos were also named on the extended bench.