You actually have several options but outside of a hard read most of them don’t normally work very well as they take too long. Against many characters if they know what they’re doing you don’t have any options except block, as if you try anything else it is easy to stuff or block.
That said, you’re options are as follows:
Regular skeleport: fully strike invulnerable on way down, no invulnerability on way up, always vulnerable to throws. Quite a slow option which can be reacted to and stuffed or even option selected to catch you coming up, even if you cancel the heavy version into another special (although you can cancel into another skeleport for more strike invulnerability).
Soul sword: has upper body invulnerability (just removes half his hurtbox) of various lengths during start up, shadow version has invulnerability last into initial active frames. Very poor as a defensive option, the invulnerability runs out before the move becomes active so it is bad as a reversal, and many attacks can hit the lower body hurtbox quite easily (including aerial attacks). Shadow version is a mediocre anti air.
Skull enhanced heavy boneshaker: beats projectiles, invulnerability starts from first frame but ends quickly after connecting, so it can’t be used to travel through a projectile if you would end up hitting on top of it.
Shadow boneshaker: throw and projectile invulnerable. Throw invulnerability is from first frame, projectile is from after the freeze so cannot be used to beat a meaty projectile. Hard read on a throw or non meaty projectile.
Shadow skeleport: fully invulnerable, long startup and very negative, always crosses up. Can be performed airborne). Can be easily blocked on reaction, and neutral jumped on reaction, both are easy punishes. Using an advancing move against Spinal (such as Jago’s double roundhouse or wind kick) will move you away from the skeleport automatically. A lot of wakeup pressure on Spinal will be attacks which allow the opponent to attack and still block this attack. Throws are an exception to this, but are also covered by shadow boneshaker.
Also, for the sake of completeness, you can avoid throws by jumping, and backdashes have a brief window of invulnerability at the start.
I most often get away with a light skeleport on wakeup if anything but it isn’t ideal and can be punished if the opponent is prepared. Mostly, you have to block and try to tech/jump throws.