It's certainly doable to reverse engineer out a cryptographic key from a chip, but most of the people who could afford to do this wouldn't really need to do so. Secure elements are typically substantially more protected than standard logic. The structures can be designed in a manner to be very difficult to access without damaging them rendering them unreadable.
Such a cryptographic key would likely be scattered in pieces around the chip, delivered through winding busses below enough critical logic connections and power rails so that the chip wouldn't be as vulnerable to a focused ion beam attack or infrared analysis. This makes it difficult to observe without destroying enough of the chip that live examination would not be possible. There are also tricks that would be used to mitigate the risk of differential power attacks etc.
The bigger threats to secure elements are sloppy design with DFT/DFM (Design For Test) features. Most complex chips have at a minimum a mechanism of connecting a large number of the designs flops to what's like a huge shift register. If you knew enough of the design you could try to locate the output of a block which has access to the secure value, scan in a vector that makes it easy to recover the value (e.g. an XOR element you can force to XOR with 0's) and scan it out.
There are also other DFT feature like on-die logic analyzers, micro-breakpoint engines, code signing overrides etc. Virtually all of these features are physically disabled prior to volume manufacturing. If a company was sloppy this could expose things that shouldn't be exposed.
There are other attacks as well though. If you could compromise the signing keys for the microcode delivered to a processor like a modern x86 processor you could change the behavior of instructions. With custom microcode you could catch and override basically any instruction (for example you could change where a LOAD instruction stores data or make ADD do jmp etc). You could definitely use something like that in a malicious manner.