The 1MB offset was chosen because it's pretty much guaranteed to be aligned, no matter the underlying storage. It was first picked when magnetic disks changed to 4KiB sectors. But aligned is aligned, and it shouldn't matter.
When I had to get my first 4K disks to work in old arrays, I'd start the partition at sector 56 (vs. the traditional 63), because moving to sector 64 wasn't possible: then the partition wouldn't be large enough to join the RAID array. On a DOS partition table, this took away some space used for GRUB, but thankfully I still had enough. Later when getting larger disks, I moved to sector 2048. The disk is larger, so the partitions can still be large enough to join the RAID arrays. Of course, having the disks in a system be different adds sysadmin work—but, well, such is life. (Thankfully, I've been able to retire most of those systems).
1MB of space on a multi-TB magnetic disk is not noticeable. Nor is it on a many-hundred-GB SSD. I confess it does irk me a little to be wasting space—I mean, I grew up in the era where 120MB was a huge hard disk, and the operating system could fit on a floppy disk. 1MB!? That's a whole operating system!
It has a huge advantage, though: It is aligned for 4K disks, it is aligned for SSDs (which have a physical block size of at least 64KiB), it is reasonably easy to make stripe-aligned on an array, and it'll probably be aligned on every reasonable storage technology for quite a while.
But if you've got a single disk, there really aren't any downsides, except being nonstandard (e.g., if I were trying to recover data a disk after a lost partition table, I'd check for the partition starting at 2048 first.)
And as for you other alternative: A non-aligned boot isn't really a huge deal. Reads might be a little slower, and writes much slower, but neither happens often at all to notice. However, a 64MB /boot partition is too small, I wouldn't go less than 256MB. Even a targeted (as opposed to generic) initrd is ~5MB, another ~4MB for the kernel, and you're quickly out of a space after a few updates (unless you've very routine about purging old kernels). EFI boot, though, should be OK as long as you're not putting kernels/initrds on there.