It's not an application like Fusion which is responsible for a proper disk alignment, it's always the operating system (or you if the operating system does not natively support creating aligned partitions). If the partitions on the physical disk are properly aligned, any files (e.g. virtual disk files) on the partition are automatically aligned too. Regarding the guest OS it's basically the same thing, if the physical partition is aligned and the guest is not, it will result in additional physical disk access.
The 1MB alignment was chosen to ensure any block size with the power of 2 (e.g. 32kB, 64kB, 256kB up to 1MB) fits, so IMO it's definitely a best practice to have the host as well as the guest aligned.
André