arrghh! there's always an Altera person lurking
Ali, if you are going to hand assemble, surely this means a very low quantity and so FPGA price does not really matter at all.
Read his posts. Each 'product' requires 200 serial linked acquisition boards, that's two hundred daughter boards, each with the cheap FPGA. If he saves 5$ in bootprom and FPGA combined, that is a 1k$ savings for each product. If he sells 10 'products', that's a 10k$ savings. If he already set his price or already quoted a final amount to his clients, for 10 installations, it is an additional 10k$ in ali_asadzadeh pocket. If he sells 100 setups, that is an additional 100k$ in his pocket. At this level, it is worth it to put in the effort to find the cheapest solution.
I'm sure the final processing unit will have some more modern FPGA which is a lot beefier.
Making everything work on a $2.15 FPGA instead of a 7$ one plus it's bootprom price in the OP ali_asadzadeh eyes may make proper business sense. And if the Altera 5M240ZT100C5N can be made to work, he may thank me for finding it as it will save him at least 1000$ for the first unit with 200 daughter boards.
For prototyping, he may only assemble 3-5 units for testing, but once the PCBs are verified error free, he will have them assembled by the PCB manufacturer.
Even the MAX10 device I listed at $4.52, which can LVDS over 650mb (the 5M240 part maxes out at 304mb) and has a full PLL will still save ali_asadzadeh over 600$ on each setup as he no longer need a boot flash, or VCC core voltage regulator to use that device. A device which has full real-time operation debug monitoring through the JTAG, PLL and a reasonable blockram unlike the cheaper altera 5M240ZT100C5N where everything need to be programed to the bone.