All of those things are solved with modern extensions. It's like comparing pre-MMX x86 code with modern x86. Misaligned loads and stores are Zicclsm, bit manipulation is Zb[abcs], atomic memory operations are made mandatory in Ziccamoa.

All of these extensions are mandatory in the RVA22 and RVA23 profiles and so will be implemented on any up to date RISC-V core. It's definitely worth setting your compiler target appropriately before making comparisons.