Your issue is because javascript (actually ECMAScript) date objects are based on a UTC time value. When you do:
new Date(<?php echo time()*1000; ?>)
you are passing a UTC millisecond time value to the Date constructor, which then creates a date object. When you use the usual Date methods to format a string, or use Date.prototpye.toString or Date.prototype.toLocaleString, you will get a string based on the client's locale. Note that all these strings are implementation dependent and vary widely for the locale version.
If you want the timezone of the server, then use the server to set it. Or you can send a time zone offset in minutes to be applied to the local time to get back to Nepalese Standard Time (UTC + 5:45). Note that in ECMAScript, the time zone offset is minutes to be added to the local time to get UTC, whereas it is more normal to define the offset in minutes to be added to UTC to get the local time.
So to get NST:
function toNST(timeValue) {
function z(n) {return (n<10? '0' : '') + n}
var d = new Date();
var nstOffset = 5 * 60 + 45;
d.setMinutes(d.getMinutes() + d.getTimezoneOffset() + nstOffset);
return z(d.getHours()) + ':' + z(d.getMinutes()) + ':' + z(d.getSeconds());
}
alert(toNST(+(new Date()))); // about 11:07:17 at the moment