It depends on the smartphone, but categorically they can't all be used as a substitute for a smart card.
Obviously, phones don't have the electromechanical interface to be inserted into the slot of a smart card reader, so they can't meet the ISO specifications that describe the pinouts, voltages, communications protocols, etc. Some phones work around this for payments by complying with a different standardized smart card communication protocol, i.e. via Near Field Communication (NFC). This is how ApplePay works. Samsung bought out LoopPay, so they are able to provide an inductive interface to mag stripe read-heads that comply with most (but not all) of the mag stripe standards. Any RF based smartcard solution requires specialized hardware that is not necessarily present in all smartphones. A Bluetooth radio or WiFi radio won't cut it.
Another place where the differences exist is in the security of the stored data. In the case of payment data, some phones have a separate "Secured Memory" which performs the encryption functions used to comply with dynamic data authentication requirements. This security module is a tiny HSM that is separate from the phone's processor, which helps prevent malicious phone apps from stealing the secret keys in the data. It is technically different than a TPM chip, which has a slightly different function. (Smart phones may not use TPM(tm) chips, but many do offer encryption of their main storage memory in a way similar to using BitLocker with a TPM chip on a PC to encrypt the hard drive.)