Almost everyone here in the Compendium thinks that the Entity created the Gates, therefore the Entity, being a sentient being, would have created the gates in places of convenience... in short, the location of these gates are arbitrary... Surely the Entity, wanting to aid Crono and Co. in defeating Lavos, would not place the gates in unsuitable places such as inside a mountian, or the sea, or a wall...
As for the Epoch, the attachment of wings by Dalton would have been an easy solution.. But how about when it was 'earthbound' so to speak? Remember that when after Zeal fell, Epoch must have been surely destroyed by the tsunami afterwards, but it wasnt.. It somehow managed to get to a place of safety, and rejoined the Co. afterwards in the Last Village.. We could assume that, being built by a wise mentor of an ancient, advanced civilization in a technologically advanced era (2300), the Epoch might contain a highly sophisticated AI that would ensure its passenger's safety, in ordinary spacetime and whilst travelling between them..