Calculating Exact TCP Overhead Cost

Corresponding this topic:

https://stackoverflow.com/questions/3613989/what-of-traffic-is-network-overhead-on-top-of-http-s-requests

The maximum segment size (which does not include the TCP or IP
headers) is typically negotiated between the layers to the size of the
MTU minus the headers size. For Ethernet MTU is usually configured at
1500 bytes. The TCP header is 160 bits, or 20 bytes. The fixed part of
the IPv4 header is 160 bits, or 20 bytes as well. … . Thus:

• for HTTP over TCP/IPv4

overhead = TCP + IP = 40 bytes

payload = 1500 – 40 = 1460 bytes

overhead % = 2% (40 * 100 / 1460)

Here's 100 Mbit and 1Gbit iperf results in TCP mode with default Debian distros:

[  5] local 10.0.51.1 port 5001 connected with 10.0.51.20 port 45009
[  5]  0.0-10.0 sec   112 MBytes  94.1 Mbits/sec
[  4] local 10.0.51.1 port 5001 connected with 10.0.51.94 port 35065
[  4]  0.0-10.0 sec  1.10 GBytes   941 Mbits/sec

I can lower it to almost 2% overhead by raising MTU to 9000 :

[ ID] Interval       Transfer     Bandwidth
[  4]  0.0-10.0 sec  1.14 GBytes   982 Mbits/sec

But shouldn't it be even less?

overhead = TCP + IP = 40 bytes
payload = 9000 - 40 = 8960 bytes
overhead % = 0.4% (40 * 100 / 8960)

Why actual "bandwidth loss" is notably greater than the theoretical?
If formula missing something valuable?