Modified bytecode, not just bytecode (or else any APK hoster would be illegal)

Any APK hoster which distributes bytecode (or any other software) without prior permission acts illegaly.

Redistribution of copyright protected material requires authorization of the right holder. Code (or programs compiled from code), usually fall under this rule.

(In the US) hoster privilege usually allows them to not be liable unless they know about a specific infraction. In some jurisdictions some platforms (such as youtube) are required to monitor uploads proactively for known copyright violations.

As noted in OP, the takedown was related to reuse of trademark (logo, name), not redistribution of the modified binary.

The comment tread is arguing that it's hard to prove modified binary rather than the easier way; reuse of the trademark. Either way, both the modification and redistribution are illegal.