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The effect of spelling rule A (ы is replaced by и) on the spelling of vowels after velar consonants is that the plain-indicator letter ы does not occur after velar consonants. The palatal-indicator letters я ё ю do not occur after velar consonants for other reasons. These restrictions on ы я ё ю apply to the language as a whole, not just to endings.
In other words,
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к, г, and х are never followed by ы, я, ё, or ю.
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The effect of the spelling rules on the spelling of vowels after the noisy consonants is that the plain-indicator letter ы does not occur after ч щ ш ж (though it does occur after ц). The palatal-indicator letters я and ю do not occur after any of the noisy consonants (including ц) for other reasons.
These restrictions on ы я ю apply to the language as a whole, not just to noun and adjective endings. In other words,
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ч, щ, ш, and ж are never followed by ы, я, or ю.
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However, rule B (unstressed о is replaced by е after a noisy consonant) applies only to noun and adjective endings; о and ё do in fact occur after the noisy consonants elsewhere, i.e. in stems and in verb endings.
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