Through the miracle of virtual machines, this is much less so. VMs are the NAT of computer systems.
One can use virtualization to help future-proof apps. IBM's System/38 (later AS/400, iSeries, and IBM i) did this for decades. However, to be fully future-proof (esp for vendor level), the virtualization SW/HW solution itself needs to be immune to the problem. That means legally, easily-cloned HW with same for software and virtualization layer. Closest thing maybe NOVA microhypervisor on Loongson-style OSS CPU with x86 emulation if it's x86 apps. RISC-V w/ virtualization support otherwise.
Guess what future-proof virtualization all the mainstream approaches aren't using, though? ;)
On the other hand this is a valid concern for containers.