Is PHP a bit 'messy'?

PHP CAN be messy, and historically it has a reputation for its users producing hideous code, both logically and syntactically but this doesn't have to be the case. The same could largely be said of Javascript in the past, because both of them were easy to pick and use, even if you had little to no idea of what you were doing.

Separating logic and presentation is a problem with most server-side languages and often necessitates some sort of framework and/or templating engine on top of a base language in order to adhere to an MVC (Model-View-Controller) pattern. This is why with Ruby you'll eventually learn Rails, with C# you'll learn MVC with ASP.NET Core.

With PHP you have options like Laravel or Zend, or other options for micro frameworks and stand-alone template engines (Slim and Twig, for example). It can still seem messy, but the language and standards within the community have matured and building well designed, modern applications is very much a viable option in PHP among the other choices.