Because you have to respect Flight Time Limitations laid out in your OM, which is approved by the respective CAA. In most companies which want to be competitive on the market, this chapter is usually copied letter-to-letter from the (in case of Europe) EU OPS Subpart Q. It is virtually the same as licencing - no sane country would try to enforce its own licensing rules for flying to their own country with foreign-registered aircraft - France did this with the age 60 rule I believe.
As for the logic behind it, you really can't compare minimums and speed limits with FTL. You have to use the higher minima for departure because not every single possible airport/runway/departure possibility is covered in law in your country. For example, a runway in some foreign country may be equipped with equipment allowing LVTO, but the charts says min. 3000m for departure - this is usually due to extensive knowledge of local weather phenomena, maybe combined with high obstacles near DER, etc.
As for the speed limits, they are usually meant as a method of managing flow into/out of a specific airport - and if most airports in one country are quite busy, it's usually more simple for the authority to say for example for all airports, at 80 DME maintain 250 kts or less - and then add exemptions to charts where this isn't neccessary.
I think implementing requirement to maintain FTLs of a specific country for overflying would be a bit of overkill and very difficult in terms of planning. I know it's a bit easier in the West with two large countries (USA and Canada) covering a lot of area, but imagine flying in Europe with lots of countries - virtually impossible and complete waste of money and time.