You can go throught the following link https://blogs.vmware.com/vsphere/2012/05/troubleshooting-storage-performance-in-vsphere-part-1-the-basics.html this would help in understanding poor storage performance is generally the result of high I/O latency
Regarding 4K alignment ratio:
As you interpreted, this graphs shows whether the I/Os are aligned to 4KB addresses or not. If the total value (red line) is always at 100%, that's the ideal situation with all I/Os aligned to 4K. Any value below 100% results in a read-modify-write or I/O splitting in the case of 512e(emulated) or 4Kn(native) drives. This implies a potential scope of improvement in workload application. But, in the case of 512n drives, this does not necessarily imply an issue. For example, a 512byte I/O which is not aligned to 4K, but aligned to a sector boundary doesn't result in any IO amplification. In some cases, this can also be due to potential issue and worth looking at it if there are significant performance regressions.
(You may ignore the vertical blue/green lines as the ratio can become zero in intervals when there is zero read/write)
Regarding the throughput spikes:
As per the graphs, there are ~50k ops of 512KB size resulting in 50GB/s and this seems unlikely. Would you please share more details on the workload that was run on the VM, drive type etc?