This では is the te-form of the copula だ, followed by the topic marker は. So it's essentially the same では in simple sentences like 私は子供ではない. Literally, ～では is "when it's ～, ..." or "if it's ～, ...".
if the appearance (of the characters) is (that of) avian species, doing 脳内再生 is difficult
those who have difficulty in doing 脳内再生 when the characters' appearance is that of avian species
for those who have difficulty in doing 脳内再生 with characters that have an avian appearance
In Hatoful Boyfriend, we have also prepared "anthropomorphized" versions of the cut-ins of the characters for those who have difficulty in doing 脳内再生 with characters that have an avian appearance.
Each character in the game is assigned a virtual seiyu, so 脳内再生 here seems to refer to imagining the characters' sweet voice without actually hearing it.