Your alarm panel will funtion properly either way. The EOL resistors are designed in the alarm system to "monitor" the line. for the line to be monitored properly they must be installed at the end of the line. The resistor reduces the amount of voltage flowing throught the line back to the panel. So when the resitor is installed anywhere in the line in series say, with window contacts (normally closed) the panel not only recognizes the closed circuit, but also a reduced voltage on the line. If a potential burgler gained access to the wiring for a zone, they could attemp to short the wiring between the panel and the contacts, thus closing the circuit & bypassing the contacts, leaving the window or door vulnerable to undetected entry. If the resistor was installed at the EOL, the resitor would also be bypassed, and the panel would recognize the change in voltage and the zone would be faulted. If the resitor was installed in the can, the short would not be detected.
I can tell you that it is difficult to install the resistor at the EOL for recessed contacts, because they must be spliced to the wire then inserted back into the hole where the contact will be placed. It is difficult to do this and keep everything intact. This is probably the reason that many residential alarm systems whether installed by pros or DIY have the resitors in the can (the control panel).
