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The nature of Plant 43's relationship with P-ε was rewritten by Flagship shortly after Resident Evil 2's release. Before Progenitor Virus was written into the series lore, the first two games featured a series of viruses, with the t-Virus being the "ε" strain of the Clay Virus. As Plant 43 was not created through this viral strain, the gas would not harm it.
In the 2019 remake of Resident Evil 2, Plant 43 was retconned into a large, room-occupying mutated plant, more directly similar to its precursor Plant 42. The in-game role of the original Plant 43 B.O.Ws has instead been given over to Ivy Zombies, which are based on Green Zombies. However, due to the nature of differing versions of the RE2 story, it is likely the Plant 43 B.O.W remains canonical.