The IRS views capital gains and losses as different from passive activity real estate gains and losses. You can tell this because your real estate losses - provided you meet certain conditions - can be used to offset regular income for a lot more than $3,000 while capital losses can't. What the code sections you're quoting have to do with is offsetting gains from the same type of investments against losses. So long term capital losses must first offset long term gains before they can be netted against short term gains. And if you have two rental properties losses from one can offset gains from the other.
Here is TurboTax's breakdown on capital gains and losses.
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