It's looks like you have very limited experience with Linux distros. Nobody forces Linux users to use repositories. We use repositories because we trust them much more than random binary blobs from Internet.
Binary encoding contribute significantly to obfuscation, because it cannot be formatted, or refactored, or commented, or modified (e.g. to add assertion or print debugging information). Nobody programs in binary.
WebAsm creates problem. Same problem as Java, Flash, Unity, PNaCl and dozens of other platforms to execute binary blobs from untrusted sources. And the only solution is to add trust, e.g. by publishing heavy-weight libraries for review and patching by third-party maintainers, e.g. such libraries as SDL, game engines, GUI, databases, etc. Otherwise, we will have same situation as with other libraries, e.g. JQuery, when sites are using old version of common library with known security problems for ages, despite that fixed version is freely available.
WebAsm creates problem. Same problem as Java, Flash, Unity, PNaCl and dozens of other platforms to execute binary blobs from untrusted sources. And the only solution is to add trust, e.g. by publishing heavy-weight libraries for review and patching by third-party maintainers, e.g. such libraries as SDL, game engines, GUI, databases, etc. Otherwise, we will have same situation as with other libraries, e.g. JQuery, when sites are using old version of common library with known security problems for ages, despite that fixed version is freely available.