ATMega ports / features - clarification

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That is correct (but the data sheet has the last word)!

USB: D- and D+ are separate pins. USART: RXD1 and TXD1 are special functions of port D bits 2 and 3 SPI: MISO, MOSI and SCK are special functions of port B bits 1, 2, and 3

So: yes, you can use all three independently and "at the same time".

(but: no, you couldn't use port D bits 2 and/or 3 together with the UART and/or port B bits 1, 2, and/or 3 together with SPI).

Josef