I think you may be confusing the VLAN database MTU and the interface MTU. Pay special attention to the note at the end. Enabling jumbo frames in the VLAN database for a VLAN will not suddenly cause all the switch interfaces in that VLAN to be enabled for jumbo frames.
Jumbo/Giant Frame Support on Catalyst Switches Configuration Example
Catalyst 6000/6500 / Cisco 7600 OSR Series
The Catalyst 6000 series and 7600 Optical Services Router (OSR)
platform can support jumbo frame sizes as of release 6.1(1) of CatOS,
and 12.1(1)E for Native IOS. However, this is dependent on the type of
line cards that you use. There are generally no restrictions to enable
the jumbo frame size feature. You can use this feature with
trunking/non-trunking and channeling/non-channeling. The default MTU
size is 9216 bytes after you enable jumbo frame support on the
individual port. However, an Application Specific Integrated Circuit
(ASIC) limitation requires that you limit the MTU size to 8092 bytes
on these 10/100-based line cards:
The WS-X6516-GE-TX is also affected at 100 Mbps. At 10/1000 Mbps, up
to 9216 bytes can be supported. However, the WS-X6548-RJ-45 line card
is not affected, as this line card uses newer ASICs.
Note: Jumbo frame support is available on WS-X6101 ATM modules.
Configure Native IOS
7609(config)#int gigabitEthernet 1/1
<1500-9216> MTU size in bytes
Verify in Native IOS
7609#show interfaces gigabitEthernet 1/1
GigabitEthernet1/1 is up, line protocol is up (connected)
Hardware is C6k 1000Mb 802.3, address is 0007.0d0e.640a (bia 0007.0d0e.640a)
MTU 9216 bytes, BW 1000000 Kbit, DLY 10 usec,
reliability 255/255, txload 1/255, rxload 1/255
The port ASICs on the Catalyst 6000 count as oversized, which are
those frames greater than 1548 bytes but less than the configured
jumbo MTU. It uses the rxOversizedPkts counter to track these frames
in the output from the show counter command. In this
case, the ifInErrors counter value increments and can equal the number
of rxOversizedPkts packets value in the show counter
command output. On a Catalyst 6000 that runs Cisco Integrated IOS
(Native Mode), use the show interface command to
check whether the input errors counter increments along with giant
counters on the interface that receives these frames.
Note: There is no relationship between the MTU value that you can specify in the VLAN database and the mtu command in the interface
configuration mode. With the VLAN database setting, the switch checks
for an MTU value greater than 1500. If the switch detects a higher
value, puts the VLAN in a non-operational state. Therefore, to support
large frames, you only need to change the interface MTU value and not
the VLAN database MTU value. If SVI is used, then in order to support
large frames, you must increase the MTU on the SVI to route the
traffic between VLANs . Refer to the Configuring Jumbo Frame
Support section of Interface Configuration for more
information about Jumbo Frame support on the Catalyst 6500.
In any case, a switch will not send out jumbo frames to an interface, even on an interface with jumbo frames enabled, unless it receives incoming jumbo frames destined for that interface.
Your concern about the
system jumbomtu command is misplaced. That command sets the non-default MTU size to which you can configure some types of interfaces, but it doesn't actually set the interface MTU size. The warning is about setting the value to the default ethernet MTU value. Doing that will change all the interfaces with non-default MTU sizes back to the default value.
The default for the
system jumbomtu is 9216, which seems to be what you want, so you should not need to change that value. If, however, you set your 10 Gb MTU to 9216, then you change the
system jumbomtu value to 1500, you will find that any interfaces where you changed the MTU to 9216 will now have an MTU" of 1500 because the
system jumbomtu is now different than what you are allowed to set the MTU.
In other words, for some types of interfaces, You can either use the default MTU of 1500, or you can change the MTU to the value set by the
system jumbomtu command, but not any other value.