Is there an alternative to .htaccess?

...in case the webhoster disabled the use of .htaccess files?

If the webhost has disabled the use of .htaccess files then there is no direct alternative. (.htaccess = per-directory Apache config file)

.htaccess files are not necessary if you have access to the Apache server config. In fact, it is preferable to use the server config instead of .htaccess anyway, but by the sounds of it, you do not have that luxury.

I can set some PHP variables and headers inside the PHP files

With PHP 5.3+ under CGI/FastCGI then you can use .user.ini files for per-directory PHP config settings. But that's just for PHP config settings, eg. error_reporting, include_path, etc. (Mind you, under CGI/FastCGI you need to use .user.ini, since you'll get a 500 internal server error if you try to use php_flag and php_value directives in .htaccess - these are for when PHP is installed as an Apache module.)

If your (shared) host has disabled .htaccess and you are wanting to do more that serve simple files then... find a new host.

Just to add, it's possible for the webhost to change the name used for per-directory Apache config files (ie. ".htaccess files") using the AccessFileName directive in the server config. However, I have never encountered a host that has done this and it might possibly break other software if it is changed. It is universally expected that the Apache per-directory config file is called ".htaccess".