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 ~, ...".
- 外見が鳥類では脳内再生が困難だ
if the appearance (of the characters) is (that of) avian species, doing 脳内再生 is difficult
- 外見が鳥類では脳内再生が困難(だ)という方
those who have difficulty in doing 脳内再生 when the characters' appearance is that of avian species
- 外見が鳥類では脳内再生が困難(だ)という方の為に
for those who have difficulty in doing 脳内再生 with characters that have an avian appearance
- はーとふる彼氏では{外見が鳥類では脳内再生が困難という方の為に}、登場人物紹介に擬人化版のカットインも御用意しました。
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.