0&1;2;3

0&amp;1<br/>2<br/>3

function func_strReplaceWithExclusion($str, $substr1, $substr2, $pass = '') {
    $encoding = ...
        
    $output = '';
    if($pass == '') {
        $output = str_replace($substr1, $substr2, $str);
        
    } else {    
        if(preg_match($str, '') === false) { $pass = '/'.preg_quote($pass, '/').'/'; }
        $strParts = preg_split($pass, $str, -1, PREG_SPLIT_OFFSET_CAPTURE);
            
        $pos = 0;
        foreach($strParts as $part) {
            $output .= mb_substr($str, $pos, $part[1] - $pos, $encoding);
            $output .= str_replace($substr1, $substr2, $part[0]);
            $pos = $part[1] + mb_strlen($part[0], $encoding);
        }
    }
    return $output;
}

if(preg_match($str, '') === false) {...}

$res = str_replace(array("/$pass/", "/$substr1/"), array("\0", $substr2), $str);

$str = '<span>0&amp;1;2;3/4/5</span>';
$substr1 = array('/', ';');
$substr2 = '<br/>';
$pass = '/(?:<[^<>]+>)|(?:\&\#?\w+;)/';  // в составе тегов и html-сущностей замена не производится
$output = func_strReplaceWithExclusion($str, $substr1, $substr2, $pass)

<span>0&amp;1<br/>2<br/>3<br/>4<br/>5</span>

$pass = '/(?:(?<=(?:^)|>)[^<>]+)|(?:\&\#?\w+;)/'  // в составе НЕтегов и html-сущностей замена не производится
$output = func_strReplaceWithExclusion($str, $substr1, $substr2, $pass)

$res = preg_replace(array("/$pass/", "/$substr1/"), array("\0", $substr2), $str);

function func_strReplaceWithExclusion($str, $substr1, $substr2, $pass = '') {
    $replaceFunc = (@preg_match($substr1, '') === false) ? 'str_replace': 'preg_replace';
    
    if($pass == '') {
        return $replaceFunc($substr1, $substr2, $str);
    } else {
        if(@preg_match($pass, '') === false) { $pass = '/'.preg_quote($pass, '/').'/'; }
        
        $output = ''; $pos = 0;
        foreach(preg_split($pass, $str, -1, PREG_SPLIT_OFFSET_CAPTURE) as $part) {
            $output .= substr($str, $pos, $part[1] - $pos).$replaceFunc($substr1, $substr2, $str);
            $pos = $part[1] + strlen($part[0]);
        }
        return $output;
    }
}

if(@preg_match($pass, '') === false) { $pass = '/'.preg_quote($pass, '/').'/'; }

$output .= substr($str, $pos, $part[1] - $pos).$replaceFunc($substr1, $substr2, $str);

function func_strReplaceWithExclusion1($str, $substr1, $substr2, $pass = '') {
    $replaceFunc = (@preg_match($substr1, '') === false) ? 'str_replace': 'preg_replace';
    
    if($pass == '') {
        return $replaceFunc($substr1, $substr2, $str);
    } else {
        if(@preg_match($pass, '') === false) { $pass = '/'.preg_quote($pass, '/').'/'; }
        
        $output = ''; $pos = 0;
        foreach(preg_split($pass, $str, -1, PREG_SPLIT_OFFSET_CAPTURE) as $part) {
            $output .= substr($str, $pos, $part[1] - $pos).$replaceFunc($substr1, $substr2, $part[0]);
            $pos = $part[1] + strlen($part[0]);
        }
        return $output;
    }
}

$str = '<span>&amp;1;2;3/4/5</span>';
$substr1 = ';';
$substr2 = '<br/>';
$pass = "/&\w+;/";

$str = '&1;2;3/4/5';
$substr1 = '/;|\//';  // регулярное выражение
$substr2 = '<br/>';
$pass = "/&\w+;/";

$str = '[MARK01] [mark02] mark03 MARK04';
$substr1 = '/(mark)\d+/i';
$substr2 = '*';
$pass = "/\[MARK\d+\]/";

[MARK01] [*] * *

[MARK01] [*] * MARK04

[MARK01] [mark02] * *

$replaceFunc = (@preg_match($substr1, '') === false) ? 'str_replace': 'preg_replace';

function func_strReplaceWithExclusion($str, $substr1, $substr2, $pass, $substrPreg = null, $passPreg = null) {
    
    $passIsRegExpr = (is_null($passIsRegExpr)? (@preg_match($pass, '') !== false): $passIsRegExpr);
    $substrIsRegExpr = (is_null($substrIsRegExpr)? (@preg_match($substr1, '') !== false): $substrIsRegExpr);
    $replaceFunc = ($substrIsRegExpr) ? 'preg_replace': 'str_replace';
    
    if($pass == '') {
        return $replaceFunc($substr1, $substr2, $str);
        
    } elseif(!$passIsRegExpr) {
        return implode($pass, $replaceFunc($substr1, $substr2, explode($pass, $str)));
        
    } else {
        $output = ''; $pos = 0;
        foreach(preg_split($pass, $str, -1, PREG_SPLIT_OFFSET_CAPTURE) as $part) {
            $output .= substr($str, $pos, $part[1] - $pos).$replaceFunc($substr1, $substr2, $part[0]);
            $pos = $part[1] + strlen($part[0]);
        }
        return $output;
    }
}

  function repl($substr1, $substr2, $str, $pass){
    preg_match_all($pass, $str, $m);
    $resArr = preg_replace($substr1, $substr2, preg_split($pass, $str));
    $res = "";
    foreach($resArr as $k=>$text){
      $res .= $text.$m[0][$k];
    }
    return $res;
  }